rs376632

Positions:

• chr6-129737925-A-G
• chr6-129737925-A-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 0.876 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.874

Alfa AF: 0.875 Hom.: 56039

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs376632; hg19: chr6-130059070;