rs9275319

Variant names:

• chr6-32698518-A-G
• rs9275319

Your query was ambiguous. Multiple possible variants found:

• chr6-32698518-A-G
• chr6-32698518-A-T

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 0.146 in 152,136 control chromosomes in the GnomAD database, including 1,908 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 0.15 (1908 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 71 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 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: 0.146 AC: 22213 AN: 152018 Hom.: 1900 Cov.: 30

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.146 AC: 22251 AN: 152136 Hom.: 1908 Cov.: 30 AF XY: 0.152 AC XY: 11322 AN XY: 74376

African (AFR) AF: 0.107 AC: 4438 AN: 41510

American (AMR) AF: 0.277 AC: 4234 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3470

East Asian (EAS) AF: 0.164 AC: 850 AN: 5178

South Asian (SAS) AF: 0.0811 AC: 391 AN: 4822

European-Finnish (FIN) AF: 0.224 AC: 2371 AN: 10580

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8815 AN: 67974

Other (OTH) AF: 0.139 AC: 295 AN: 2116

Alfa AF: 0.141 Hom.: 3610

Bravo AF: 0.155

Asia WGS AF: 0.111 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.5
DANN	Benign	0.16
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs9275319; hg19: chr6-32666295;