rs11175885

Variant names:

• chr12-65720850-A-G
• rs11175885

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 0.672 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

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 = 0.911 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: 0.673 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

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.735

Alfa AF: 0.840 Hom.: 54942

Bravo AF: 0.636

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11175885; hg19: chr12-66114630;