9-110629206-T-A

Variant names:

• chr9-110629206-T-A
• rs9657655

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 0.749 in 151,958 control chromosomes in the GnomAD database, including 43,491 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 0.75 (43491 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 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: 0.749 AC: 113683 AN: 151840 Hom.: 43452 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.749 AC: 113775 AN: 151958 Hom.: 43491 Cov.: 31 AF XY: 0.756 AC XY: 56126 AN XY: 74250

African (AFR) AF: 0.596 AC: 24697 AN: 41448

American (AMR) AF: 0.808 AC: 12301 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2763 AN: 3472

East Asian (EAS) AF: 0.980 AC: 5079 AN: 5184

South Asian (SAS) AF: 0.824 AC: 3966 AN: 4816

European-Finnish (FIN) AF: 0.887 AC: 9387 AN: 10578

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53187 AN: 67924

Other (OTH) AF: 0.752 AC: 1590 AN: 2114

Alfa AF: 0.726 Hom.: 2347

Bravo AF: 0.737

Asia WGS AF: 0.880 AC: 3048 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.31
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs9657655; hg19: chr9-113391486;