9-133175167-T-C

Variant names:

• chr9-133175167-T-C
• rs7850541

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 0.798 in 152,222 control chromosomes in the GnomAD database, including 48,675 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 0.80 (48675 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121383 AN: 152104 Hom.: 48631 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.798 AC: 121482 AN: 152222 Hom.: 48675 Cov.: 33 AF XY: 0.802 AC XY: 59709 AN XY: 74432

African (AFR) AF: 0.835 AC: 34684 AN: 41524

American (AMR) AF: 0.795 AC: 12152 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2665 AN: 3472

East Asian (EAS) AF: 0.714 AC: 3703 AN: 5186

South Asian (SAS) AF: 0.823 AC: 3970 AN: 4822

European-Finnish (FIN) AF: 0.867 AC: 9197 AN: 10604

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52537 AN: 68002

Other (OTH) AF: 0.770 AC: 1627 AN: 2114

Alfa AF: 0.778 Hom.: 13655

Bravo AF: 0.795

Asia WGS AF: 0.781 AC: 2714 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.67
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7850541; hg19: chr9-136050554;