rs9271117

Variant names:

• chr6-32609018-C-T
• rs9271117

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.72 (33162 hom., cov: 18)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Homozygotes in GnomAd4 at 33162 gene

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: 0.723 AC: 90166 AN: 124796 Hom.: 33144 Cov.: 18

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.722 AC: 90209 AN: 124862 Hom.: 33162 Cov.: 18 AF XY: 0.715 AC XY: 42717 AN XY: 59768

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.740 AC: 24166 AN: 32640

American (AMR) AF: 0.755 AC: 8807 AN: 11670

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2351 AN: 3024

East Asian (EAS) AF: 0.795 AC: 3558 AN: 4476

South Asian (SAS) AF: 0.682 AC: 2484 AN: 3640

European-Finnish (FIN) AF: 0.601 AC: 4812 AN: 8006

Middle Eastern (MID) AF: 0.852 AC: 225 AN: 264

European-Non Finnish (NFE) AF: 0.717 AC: 42061 AN: 58702

Other (OTH) AF: 0.742 AC: 1231 AN: 1660

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.737 Hom.: 67600

Asia WGS AF: 0.711 AC: 2470 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.83
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9271117; hg19: chr6-32576795;