18-812712-C-A

Variant names:

• chr18-812712-C-A
• rs7233932
• ENST00000610185.3:n.336C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000610185.3(ENSG00000273355):​n.336C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ENSG00000273355 ENST00000610185.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 2 publications found

Genes affected

ENSG00000273355 (HGNC:):

YES1 (HGNC:12841): (YES proto-oncogene 1, Src family tyrosine kinase) This gene is the cellular homolog of the Yamaguchi sarcoma virus oncogene. The encoded protein has tyrosine kinase activity and belongs to the src family of proteins. This gene lies in close proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YES1	XM_024451244.2	c.-51G>T		5_prime_UTR_variant	Exon 1 of 12		XP_024307012.1
YES1	XM_047437770.1	c.-51G>T		5_prime_UTR_variant	Exon 1 of 11		XP_047293726.1
YES1	XM_024451243.2	c.-337G>T		upstream_gene_variant			XP_024307011.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000273355	ENST00000610185.3	n.336C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000273355	ENST00000832908.1	n.79+188C>A		intron_variant	Intron 1 of 1
ENSG00000273355	ENST00000832909.1	n.28+188C>A		intron_variant	Intron 1 of 1
YES1	ENST00000584307.5	c.-337G>T		upstream_gene_variant		1		ENSP00000462468.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.8
DANN	Benign	0.60
PhyloP100		-0.42
PromoterAI		-0.0023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7233932; hg19: chr18-812713;