rs9276601

Variant names:

• chr6-32766527-A-G
• rs9276601

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 0.158 in 105,538 control chromosomes in the GnomAD database, including 1,255 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 0.16 (1255 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 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: 0.158 AC: 16652 AN: 105444 Hom.: 1254 Cov.: 32

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.0917

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.158 AC: 16642 AN: 105538 Hom.: 1255 Cov.: 32 AF XY: 0.156 AC XY: 8002 AN XY: 51284

Gnomad4 AFR AF: 0.0397

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0282

Gnomad4 SAS AF: 0.0908

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.168

Alfa AF: 0.139 Hom.: 1078

Bravo AF: 0.0968

Asia WGS AF: 0.0380 AC: 133 AN: 3420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9276601; hg19: chr6-32734304;