9-29626139-T-G

Variant names:

• chr9-29626139-T-G
• rs1930395

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.899 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

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.906

Alfa AF: 0.926 Hom.: 79720

Bravo AF: 0.888

Asia WGS AF: 0.934 AC: 3250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1930395; hg19: chr9-29626137;