rs11170234

Variant names:

• chr12-52685590-G-A
• rs11170234

Your query was ambiguous. Multiple possible variants found:

• chr12-52685590-G-A
• chr12-52685590-G-C
• chr12-52685590-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 0.46 in 152,078 control chromosomes in the GnomAD database, including 16,299 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 0.46 (16299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 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: 0.460 AC: 69864 AN: 151960 Hom.: 16260 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.460 AC: 69948 AN: 152078 Hom.: 16299 Cov.: 32 AF XY: 0.456 AC XY: 33888 AN XY: 74362

African (AFR) AF: 0.470 AC: 19499 AN: 41468

American (AMR) AF: 0.424 AC: 6485 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1230 AN: 5168

South Asian (SAS) AF: 0.476 AC: 2292 AN: 4818

European-Finnish (FIN) AF: 0.466 AC: 4932 AN: 10582

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32106 AN: 67954

Other (OTH) AF: 0.441 AC: 933 AN: 2116

Alfa AF: 0.310 Hom.: 727

Bravo AF: 0.456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.32
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs11170234; hg19: chr12-53079374;