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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.356

Alfa AF: 0.341 Hom.: 17955

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

Splicing

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

Publications

LitVar

Other links and lift over

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