rs9267955

chr6-32245373-A-Gchr6-32245373-A-T

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 0.89 in 152,324 control chromosomes in the GnomAD database, including 60,387 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 0.89 (60387 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135421 AN: 152206 Hom.: 60339 Cov.: 35

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.966

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.890 AC: 135528 AN: 152324 Hom.: 60387 Cov.: 35 AF XY: 0.892 AC XY: 66428 AN XY: 74488

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.966

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.979

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.911

Alfa AF: 0.864 Hom.: 14340

Bravo AF: 0.893

Asia WGS AF: 0.977 AC: 3397 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	5.1
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9267955; hg19: chr6-32213150;