rs9267502

Variant names:

• chr6-31585417-G-A
• rs9267502

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 0.0763 in 152,096 control chromosomes in the GnomAD database, including 483 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 0.076 (483 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0788 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: 0.0762 AC: 11577 AN: 151978 Hom.: 479 Cov.: 30

Gnomad AFR AF: 0.0806

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0779

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0267

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0789

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0763 AC: 11601 AN: 152096 Hom.: 483 Cov.: 30 AF XY: 0.0741 AC XY: 5513 AN XY: 74352

African (AFR) AF: 0.0811 AC: 3363 AN: 41472

American (AMR) AF: 0.0778 AC: 1189 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3466

East Asian (EAS) AF: 0.0268 AC: 139 AN: 5186

South Asian (SAS) AF: 0.0843 AC: 406 AN: 4816

European-Finnish (FIN) AF: 0.0197 AC: 208 AN: 10568

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0789 AC: 5366 AN: 67998

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

Alfa AF: 0.0750 Hom.: 147

Bravo AF: 0.0810

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9267502; hg19: chr6-31553194;