rs9271170

Variant names:

• chr6-32610112-T-C
• rs9271170

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 0.745 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
• Publications: 39 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 (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

African (AFR) AF: 0.768 AC: 31772 AN: 41374

American (AMR) AF: 0.787 AC: 12034 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2728 AN: 3468

East Asian (EAS) AF: 0.803 AC: 4147 AN: 5162

South Asian (SAS) AF: 0.728 AC: 3510 AN: 4820

European-Finnish (FIN) AF: 0.657 AC: 6910 AN: 10518

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.729 AC: 49450 AN: 67854

Other (OTH) AF: 0.770 AC: 1621 AN: 2106

Alfa AF: 0.742 Hom.: 73701

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

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