SH2D3C p.Ala695Ala

Variant names:

• chr9-127741790-G-G
• NM_170600.3:c.

Your query was ambiguous. Multiple possible variants found:

• chr9-127741791--
• chr9-127741791-G-A
• chr9-127741791-G-T
• chr9-127741791-G-C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_170600.3(SH2D3C):​c. variant causes a splice region, exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SH2D3C NM_170600.3 splice_region, exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 0 publications found

Genes affected

SH2D3C (HGNC:16884): (SH2 domain containing 3C) This gene encodes an adaptor protein and member of a cytoplasmic protein family involved in cell migration. The encoded protein contains a putative Src homology 2 (SH2) domain and guanine nucleotide exchange factor-like domain which allows this signaling protein to form a complex with scaffolding protein Crk-associated substrate. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_170600.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SH2D3C	NM_170600.3	MANE Select	c.		splice_region exon_region	Exon 9 of 12	NP_733745.1	Q8N5H7-1
	SH2D3C	NM_001252334.2		c.		splice_region exon_region	Exon 9 of 12	NP_001239263.1	Q8N5H7-4
	SH2D3C	NM_005489.4		c.		splice_region exon_region	Exon 8 of 11	NP_005480.2	Q8N5H7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SH2D3C	ENST00000314830.13	TSL:1 MANE Select	c.		splice_region exon_region	Exon 9 of 12	ENSP00000317817.8	Q8N5H7-1
	SH2D3C	ENST00000373276.7	TSL:1	c.		splice_region exon_region	Exon 9 of 12	ENSP00000362373.3	Q8N5H7-4
	SH2D3C	ENST00000373277.8	TSL:1	c.		splice_region exon_region	Exon 8 of 11	ENSP00000362374.4	Q8N5H7-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 60

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.097

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr9-130504069;