rs7929469

Variant names:

• chr11-9563712-G-A
• rs7929469

Your query was ambiguous. Multiple possible variants found:

• chr11-9563712-G-A
• chr11-9563712-G-C
• chr11-9563712-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.768 AC: 31879 AN: 41502

American (AMR) AF: 0.887 AC: 13576 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2614 AN: 3472

East Asian (EAS) AF: 0.725 AC: 3736 AN: 5156

South Asian (SAS) AF: 0.709 AC: 3418 AN: 4824

European-Finnish (FIN) AF: 0.935 AC: 9912 AN: 10604

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61504 AN: 68010

Other (OTH) AF: 0.846 AC: 1785 AN: 2110

Alfa AF: 0.867 Hom.: 18490

Bravo AF: 0.844

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.52
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs7929469; hg19: chr11-9585259;