chr6-32607958-A-G

Variant names:

• chr6-32607958-A-G
• rs9461776

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 0.0884 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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0912 AC: 3773 AN: 41382

American (AMR) AF: 0.0791 AC: 1208 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3466

East Asian (EAS) AF: 0.0652 AC: 337 AN: 5170

South Asian (SAS) AF: 0.0772 AC: 372 AN: 4816

European-Finnish (FIN) AF: 0.0378 AC: 401 AN: 10606

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.0929 AC: 6307 AN: 67886

Other (OTH) AF: 0.100 AC: 212 AN: 2110

Alfa AF: 0.0912 Hom.: 1284

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
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs9461776; hg19: chr6-32575735;