Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_007373.3(SHOC2):c.1302C>T (p.Asn434=)

CA293482

139108 (ClinVar)

Gene: SHOC2
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: ba4e5908-3b34-42d0-8df7-f0b029ff11e2
Approved on: 2017-04-03
Published on: 2018-12-10

HGVS expressions

NM_007373.3:c.1302C>T
NM_007373.3(SHOC2):c.1302C>T (p.Asn434=)
NC_000010.11:g.111009265C>T
CM000672.2:g.111009265C>T
NC_000010.10:g.112769023C>T
CM000672.1:g.112769023C>T
NC_000010.9:g.112759013C>T
NG_028922.1:g.94723C>T
NM_001269039.1:c.1164C>T
NM_001269039.2:c.1164C>T
NM_001324336.1:c.1302C>T
NM_001324337.1:c.1302C>T
NR_136749.1:n.714C>T
ENST00000265277.9:c.1164C>T
ENST00000369452.8:c.1302C>T
ENST00000451838.1:n.672C>T
ENST00000489390.1:n.516C>T

Benign

Met criteria codes 4
BA1 BP7 BP5 BP4
Not Met criteria codes 1
BP2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.1302C>T (p.Asn434=) variant in the SHOC2 gene has been identified in a patient with an alternate molecular basis for disease (BP5; ClinVar SCV000171633.12). The silent p.Asn434= variant is not predicted by MaxEntScan to impact splicing (BP7, BP4).The filtering allele frequency of the c.1302C>T (p.Asn434=) variant is 0.74% for African chromosomes by the Exome Aggregation Consortium (87/9772 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BA1, BP5, BP4, BP7.
Met criteria codes
BA1
The filtering allele frequency of the c.1302C>T (p.Asn434=) variant is 0.74% for African chromosomes by the Exome Aggregation Consortium (87/9772 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1)
BP7
The silent XXX variant in GENE is not predicted by MaxEntScan to impact splicing (BP7, BP4).
BP5
The c.1302C>T (p.Asn434=) variant in the SHOC2 gene has been identified in a patient with an alternate molecular basis for disease (BP5; ClinVar SCV000171633.12)
BP4
The silent XXX variant in GENE is not predicted by MaxEntScan to impact splicing (BP7, BP4).
Not Met criteria codes
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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