rs376632

Variant names:

• chr6-129737925-A-G
• rs376632

Your query was ambiguous. Multiple possible variants found:

• chr6-129737925-A-G
• chr6-129737925-A-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 0.876 in 152,166 control chromosomes in the GnomAD database, including 58,491 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 0.88 (58491 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.882 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: 0.876 AC: 133238 AN: 152048 Hom.: 58440 Cov.: 31

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.876 AC: 133348 AN: 152166 Hom.: 58491 Cov.: 31 AF XY: 0.875 AC XY: 65119 AN XY: 74416

African (AFR) AF: 0.854 AC: 35444 AN: 41488

American (AMR) AF: 0.894 AC: 13680 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3174 AN: 3472

East Asian (EAS) AF: 0.850 AC: 4400 AN: 5178

South Asian (SAS) AF: 0.849 AC: 4092 AN: 4820

European-Finnish (FIN) AF: 0.909 AC: 9628 AN: 10594

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60026 AN: 67998

Other (OTH) AF: 0.874 AC: 1845 AN: 2112

Alfa AF: 0.876 Hom.: 74036

Bravo AF: 0.873

Asia WGS AF: 0.832 AC: 2885 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs376632; hg19: chr6-130059070;