9-29626139-T-G

Variant names:

• chr9-29626139-T-G
• rs1930395

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 0.899 in 152,092 control chromosomes in the GnomAD database, including 61,656 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 0.90 (61656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136624 AN: 151974 Hom.: 61610 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.899 AC: 136721 AN: 152092 Hom.: 61656 Cov.: 32 AF XY: 0.899 AC XY: 66853 AN XY: 74354

African (AFR) AF: 0.828 AC: 34250 AN: 41384

American (AMR) AF: 0.857 AC: 13110 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3286 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5163 AN: 5172

South Asian (SAS) AF: 0.880 AC: 4240 AN: 4820

European-Finnish (FIN) AF: 0.936 AC: 9933 AN: 10608

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.937 AC: 63736 AN: 68028

Other (OTH) AF: 0.906 AC: 1916 AN: 2114

Alfa AF: 0.924 Hom.: 109576

Bravo AF: 0.888

Asia WGS AF: 0.934 AC: 3250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1930395; hg19: chr9-29626137;