rs12071124

Variant names:

• chr1-241520405-C-A
• rs12071124

Your query was ambiguous. Multiple possible variants found:

• chr1-241520405-C-A
• chr1-241520405-C-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 0.705 in 151,422 control chromosomes in the GnomAD database, including 37,798 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 0.71 (37798 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.81 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: 0.705 AC: 106719 AN: 151308 Hom.: 37779 Cov.: 29

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.705 AC: 106791 AN: 151422 Hom.: 37798 Cov.: 29 AF XY: 0.708 AC XY: 52370 AN XY: 73978

African (AFR) AF: 0.649 AC: 26750 AN: 41204

American (AMR) AF: 0.683 AC: 10412 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2444 AN: 3462

East Asian (EAS) AF: 0.572 AC: 2949 AN: 5152

South Asian (SAS) AF: 0.832 AC: 4000 AN: 4808

European-Finnish (FIN) AF: 0.775 AC: 8049 AN: 10380

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49813 AN: 67870

Other (OTH) AF: 0.695 AC: 1456 AN: 2094

Alfa AF: 0.675 Hom.: 2349

Bravo AF: 0.686

Asia WGS AF: 0.712 AC: 2469 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.36
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs12071124; hg19: chr1-241683705;