rs4715332

Variant names:

• chr6-52804387-C-A
• rs4715332

Your query was ambiguous. Multiple possible variants found:

• chr6-52804387-C-A
• chr6-52804387-C-G
• chr6-52804387-C-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 0.635 in 152,016 control chromosomes in the GnomAD database, including 31,274 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 0.64 (31274 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.635 AC: 96484 AN: 151898 Hom.: 31253 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.635 AC: 96553 AN: 152016 Hom.: 31274 Cov.: 32 AF XY: 0.638 AC XY: 47429 AN XY: 74294

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.634

Alfa AF: 0.589 Hom.: 45417

Bravo AF: 0.648

Asia WGS AF: 0.741 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4715332; hg19: chr6-52669185;