9-119719629-T-G

Variant names:

• chr9-119719629-T-G
• rs4642724

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 0.913 in 152,162 control chromosomes in the GnomAD database, including 63,444 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 0.91 (63444 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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: 0.913 AC: 138783 AN: 152044 Hom.: 63407 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.913 AC: 138878 AN: 152162 Hom.: 63444 Cov.: 32 AF XY: 0.915 AC XY: 68039 AN XY: 74394

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.937

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.943

Gnomad4 NFE AF: 0.925

Gnomad4 OTH AF: 0.915

Alfa AF: 0.924 Hom.: 70072

Bravo AF: 0.911

Asia WGS AF: 0.915 AC: 3183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4642724; hg19: chr9-122481907;