rs9275326

Variant names:

• chr6-32698883-C-T
• rs9275326

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 0.0919 in 152,180 control chromosomes in the GnomAD database, including 812 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 0.092 (812 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 42 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.175 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: 0.0918 AC: 13958 AN: 152062 Hom.: 811 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0925

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

GnomAD4 genome AF: 0.0919 AC: 13978 AN: 152180 Hom.: 812 Cov.: 32 AF XY: 0.0937 AC XY: 6970 AN XY: 74398

African (AFR) AF: 0.0373 AC: 1548 AN: 41544

American (AMR) AF: 0.180 AC: 2757 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3462

East Asian (EAS) AF: 0.0764 AC: 396 AN: 5184

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4822

European-Finnish (FIN) AF: 0.111 AC: 1178 AN: 10594

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6841 AN: 67988

Other (OTH) AF: 0.0916 AC: 193 AN: 2108

Alfa AF: 0.101 Hom.: 1362

Bravo AF: 0.0987

Asia WGS AF: 0.0600 AC: 211 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	12
DANN	Benign	0.59
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs9275326; hg19: chr6-32666660;