5-50937365-T-C

Variant names:

• chr5-50937365-T-C
• rs151997

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.667

Alfa AF: 0.628 Hom.: 14430

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

Splicing

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

Publications

LitVar

Other links and lift over

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