rs9276601

Variant names:

• chr6-32766527-A-G
• rs9276601

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 0.158 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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0397 AC: 1022 AN: 25774

American (AMR) AF: 0.142 AC: 1429 AN: 10032

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 381 AN: 2386

East Asian (EAS) AF: 0.0282 AC: 74 AN: 2626

South Asian (SAS) AF: 0.0908 AC: 284 AN: 3128

European-Finnish (FIN) AF: 0.254 AC: 1901 AN: 7492

Middle Eastern (MID) AF: 0.190 AC: 33 AN: 174

European-Non Finnish (NFE) AF: 0.216 AC: 11227 AN: 52066

Other (OTH) AF: 0.168 AC: 227 AN: 1352

Alfa AF: 0.146 Hom.: 2681

Bravo AF: 0.0968

Asia WGS AF: 0.0380 AC: 133 AN: 3420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.9
DANN	Benign	0.58
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs9276601; hg19: chr6-32734304;