18-812712-C-G

Variant names:

• chr18-812712-C-G
• rs7233932
• XM_024451244.2:c.-51G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_024451244.2(YES1):​c.-51G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,058 control chromosomes in the GnomAD database, including 11,091 homozygotes. 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: 𝑓 0.37 (11091 hom., cov: 32)
• Consequence: YES1 XM_024451244.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

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]

ENSG00000273355 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000273355	ENST00000610185.2	n.325C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
YES1	ENST00000584307.5	c.-337G>C		upstream_gene_variant		1		ENSP00000462468.1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56345 AN: 151940 Hom.: 11081 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.371 AC: 56403 AN: 152058 Hom.: 11091 Cov.: 32 AF XY: 0.370 AC XY: 27472 AN XY: 74340

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.349

Alfa AF: 0.342 Hom.: 1156

Bravo AF: 0.390

Asia WGS AF: 0.383 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7233932; hg19: chr18-812713;