rs7929469

chr11-9563712-G-Achr11-9563712-G-Cchr11-9563712-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 0.851 in 152,186 control chromosomes in the GnomAD database, including 55,619 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 0.85 (55619 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 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: 0.852 AC: 129489 AN: 152068 Hom.: 55598 Cov.: 31

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.851 AC: 129558 AN: 152186 Hom.: 55619 Cov.: 31 AF XY: 0.850 AC XY: 63252 AN XY: 74416

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.935

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.846

Alfa AF: 0.881 Hom.: 8954

Bravo AF: 0.844

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.8
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7929469; hg19: chr11-9585259;