rs960312

chr9-117681501-G-Achr9-117681501-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 0.822 in 151,468 control chromosomes in the GnomAD database, including 51,462 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 (51462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124426 AN: 151350 Hom.: 51415 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.822 AC: 124531 AN: 151468 Hom.: 51462 Cov.: 32 AF XY: 0.818 AC XY: 60498 AN XY: 73978

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.839

Alfa AF: 0.855 Hom.: 82296

Bravo AF: 0.829

Asia WGS AF: 0.831 AC: 2885 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	5.1
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs960312; hg19: chr9-120443779;