rs1167125

Variant names:

• chr12-43040479-C-A
• rs1167125
• ENST00000770502.1:n.95-12304C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-43040479-C-A
• chr12-43040479-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000770502.1(ENSG00000257849):​n.95-12304C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 152,148 control chromosomes in the GnomAD database, including 67,035 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 0.94 (67035 hom., cov: 31)
• Consequence: ENSG00000257849 ENST00000770502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 4 publications found

Genes affected

ENSG00000257849 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.936 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
ENSG00000257849	ENST00000770502.1	n.95-12304C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142643 AN: 152030 Hom.: 66986 Cov.: 31

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.938 AC: 142750 AN: 152148 Hom.: 67035 Cov.: 31 AF XY: 0.940 AC XY: 69936 AN XY: 74380

African (AFR) AF: 0.920 AC: 38230 AN: 41538

American (AMR) AF: 0.949 AC: 14470 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3156 AN: 3470

East Asian (EAS) AF: 0.947 AC: 4903 AN: 5176

South Asian (SAS) AF: 0.944 AC: 4559 AN: 4828

European-Finnish (FIN) AF: 0.988 AC: 10486 AN: 10610

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63858 AN: 67966

Other (OTH) AF: 0.929 AC: 1962 AN: 2112

Alfa AF: 0.938 Hom.: 186555

Bravo AF: 0.934

Asia WGS AF: 0.941 AC: 3254 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.45
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1167125; hg19: chr12-43434282; COSMIC: COSV62490409;