rs11175885

Variant names:

• chr12-65720850-A-G
• rs11175885

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 0.672 in 152,172 control chromosomes in the GnomAD database, including 41,258 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 0.67 (41258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 8 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 = 0.911 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: 0.673 AC: 102278 AN: 152054 Hom.: 41271 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.672 AC: 102255 AN: 152172 Hom.: 41258 Cov.: 32 AF XY: 0.667 AC XY: 49649 AN XY: 74404

African (AFR) AF: 0.234 AC: 9728 AN: 41484

American (AMR) AF: 0.675 AC: 10322 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3297 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1481 AN: 5154

South Asian (SAS) AF: 0.696 AC: 3360 AN: 4828

European-Finnish (FIN) AF: 0.856 AC: 9092 AN: 10620

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62391 AN: 68010

Other (OTH) AF: 0.735 AC: 1551 AN: 2110

Alfa AF: 0.806 Hom.: 147861

Bravo AF: 0.636

Asia WGS AF: 0.443 AC: 1540 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	1.2
DANN	Benign	0.34
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11175885; hg19: chr12-66114630;