rs9267502

Variant names:

• chr6-31585417-G-A
• rs9267502

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 0.0763 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0811

Gnomad4 AMR AF: 0.0778

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0268

Gnomad4 SAS AF: 0.0843

Gnomad4 FIN AF: 0.0197

Gnomad4 NFE AF: 0.0789

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0751 Hom.: 63

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9267502; hg19: chr6-31553194;