rs1153188

Variant names:

• chr12-54705212-T-A
• rs1153188

Your query was ambiguous. Multiple possible variants found:

• chr12-54705212-T-A
• chr12-54705212-T-C
• chr12-54705212-T-G

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 0.763 in 152,096 control chromosomes in the GnomAD database, including 44,495 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 0.76 (44495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 60 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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: 0.763 AC: 115989 AN: 151978 Hom.: 44434 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.763 AC: 116108 AN: 152096 Hom.: 44495 Cov.: 32 AF XY: 0.766 AC XY: 56955 AN XY: 74362

African (AFR) AF: 0.762 AC: 31624 AN: 41492

American (AMR) AF: 0.831 AC: 12712 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2597 AN: 3470

East Asian (EAS) AF: 0.976 AC: 5058 AN: 5180

South Asian (SAS) AF: 0.817 AC: 3933 AN: 4816

European-Finnish (FIN) AF: 0.700 AC: 7399 AN: 10566

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50259 AN: 67966

Other (OTH) AF: 0.770 AC: 1626 AN: 2112

Alfa AF: 0.754 Hom.: 24035

Bravo AF: 0.776

Asia WGS AF: 0.880 AC: 3059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.75
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1153188; hg19: chr12-55098996;