rs1317632

Variant names:

• chr5-66450640-G-A
• rs1317632

Your query was ambiguous. Multiple possible variants found:

• chr5-66450640-G-A
• chr5-66450640-G-T

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 0.372 in 151,998 control chromosomes in the GnomAD database, including 10,720 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 (10720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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: 0.372 AC: 56444 AN: 151880 Hom.: 10720 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.372 AC: 56477 AN: 151998 Hom.: 10720 Cov.: 32 AF XY: 0.370 AC XY: 27526 AN XY: 74304

African (AFR) AF: 0.447 AC: 18533 AN: 41440

American (AMR) AF: 0.367 AC: 5605 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3464

East Asian (EAS) AF: 0.430 AC: 2222 AN: 5162

South Asian (SAS) AF: 0.367 AC: 1770 AN: 4822

European-Finnish (FIN) AF: 0.306 AC: 3227 AN: 10562

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23093 AN: 67962

Other (OTH) AF: 0.356 AC: 752 AN: 2110

Alfa AF: 0.344 Hom.: 26647

Bravo AF: 0.381

Asia WGS AF: 0.347 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.55
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1317632; hg19: chr5-65746468; COSMIC: COSV60149863;