5-151018400-C-T

Variant names:

• chr5-151018400-C-T
• rs3763013

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 0.541 in 151,944 control chromosomes in the GnomAD database, including 25,188 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 0.54 (25188 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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: 0.541 AC: 82169 AN: 151824 Hom.: 25174 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.541 AC: 82196 AN: 151944 Hom.: 25188 Cov.: 31 AF XY: 0.545 AC XY: 40462 AN XY: 74252

African (AFR) AF: 0.228 AC: 9457 AN: 41424

American (AMR) AF: 0.669 AC: 10224 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2170 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3724 AN: 5166

South Asian (SAS) AF: 0.563 AC: 2695 AN: 4784

European-Finnish (FIN) AF: 0.673 AC: 7110 AN: 10560

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44936 AN: 67954

Other (OTH) AF: 0.552 AC: 1164 AN: 2110

Alfa AF: 0.615 Hom.: 45821

Bravo AF: 0.531

Asia WGS AF: 0.588 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.38
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs3763013; hg19: chr5-150397961;