chr9-7909576-G-T

Position:

• chr9-7909576-G-T

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 0.818 in 152,080 control chromosomes in the GnomAD database, including 51,367 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 0.82 (51367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124215 AN: 151962 Hom.: 51303 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.818 AC: 124341 AN: 152080 Hom.: 51367 Cov.: 32 AF XY: 0.815 AC XY: 60577 AN XY: 74294

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.794

Alfa AF: 0.767 Hom.: 58431

Bravo AF: 0.826

Asia WGS AF: 0.885 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7849795; hg19: chr9-7909576;