chr11-9563712-G-A

Variant names:

• chr11-9563712-G-A
• rs7929469

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;