9-134924613-C-T

Variant names:

• chr9-134924613-C-T
• rs2094962

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 0.246 in 152,088 control chromosomes in the GnomAD database, including 7,836 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 0.25 (7836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37368 AN: 151970 Hom.: 7817 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.246 AC: 37422 AN: 152088 Hom.: 7836 Cov.: 32 AF XY: 0.239 AC XY: 17783 AN XY: 74354

African (AFR) AF: 0.575 AC: 23822 AN: 41450

American (AMR) AF: 0.141 AC: 2153 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3466

East Asian (EAS) AF: 0.135 AC: 700 AN: 5168

South Asian (SAS) AF: 0.128 AC: 618 AN: 4818

European-Finnish (FIN) AF: 0.0847 AC: 897 AN: 10590

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7951 AN: 68000

Other (OTH) AF: 0.229 AC: 483 AN: 2110

Alfa AF: 0.164 Hom.: 10192

Bravo AF: 0.267

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.30
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2094962; hg19: chr9-137816459;