rs9271170

Variant names:

• chr6-32610112-T-C
• rs9271170

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 0.745 in 151,784 control chromosomes in the GnomAD database, including 42,265 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 0.74 (42265 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

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 (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.745 AC: 112958 AN: 151666 Hom.: 42230 Cov.: 31

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.745 AC: 113044 AN: 151784 Hom.: 42265 Cov.: 31 AF XY: 0.742 AC XY: 55035 AN XY: 74170

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.770

Alfa AF: 0.741 Hom.: 36577

Bravo AF: 0.759

Asia WGS AF: 0.710 AC: 2473 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	6.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9271170; hg19: chr6-32577889; COSMIC: COSV57176245;