chr5-50937365-T-C

Variant names:

• chr5-50937365-T-C
• rs151997

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.645 in 152,056 control chromosomes in the GnomAD database, including 32,016 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 0.65 (32016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98012 AN: 151938 Hom.: 31976 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.645 AC: 98114 AN: 152056 Hom.: 32016 Cov.: 32 AF XY: 0.644 AC XY: 47826 AN XY: 74312

African (AFR) AF: 0.675 AC: 27989 AN: 41466

American (AMR) AF: 0.706 AC: 10775 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3472

East Asian (EAS) AF: 0.855 AC: 4418 AN: 5166

South Asian (SAS) AF: 0.753 AC: 3628 AN: 4818

European-Finnish (FIN) AF: 0.543 AC: 5746 AN: 10578

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41180 AN: 67970

Other (OTH) AF: 0.667 AC: 1408 AN: 2110

Alfa AF: 0.633 Hom.: 21283

Bravo AF: 0.659

Asia WGS AF: 0.802 AC: 2789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.47
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs151997; hg19: chr5-50233199; COSMIC: COSV72718185;