rs9461776

Positions:

• chr6-32607958-A-G

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 0.0884 in 151,914 control chromosomes in the GnomAD database, including 744 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 0.088 (744 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.941

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.091 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: 0.0884 AC: 13419 AN: 151792 Hom.: 745 Cov.: 30

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0884 AC: 13426 AN: 151914 Hom.: 744 Cov.: 30 AF XY: 0.0862 AC XY: 6401 AN XY: 74296

Gnomad4 AFR AF: 0.0912

Gnomad4 AMR AF: 0.0791

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.0652

Gnomad4 SAS AF: 0.0772

Gnomad4 FIN AF: 0.0378

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0960 Hom.: 268

Bravo AF: 0.0924

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	16
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9461776; hg19: chr6-32575735;