rs1493829

Variant names:

• chr12-74590978-C-A
• rs1493829

Your query was ambiguous. Multiple possible variants found:

• chr12-74590978-C-A
• chr12-74590978-C-G
• chr12-74590978-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 0.717 in 152,000 control chromosomes in the GnomAD database, including 39,560 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 0.72 (39560 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.94 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: 0.717 AC: 108957 AN: 151882 Hom.: 39529 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.717 AC: 109041 AN: 152000 Hom.: 39560 Cov.: 32 AF XY: 0.725 AC XY: 53859 AN XY: 74328

African (AFR) AF: 0.659 AC: 27339 AN: 41460

American (AMR) AF: 0.761 AC: 11627 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2170 AN: 3464

East Asian (EAS) AF: 0.962 AC: 4981 AN: 5178

South Asian (SAS) AF: 0.879 AC: 4244 AN: 4826

European-Finnish (FIN) AF: 0.769 AC: 8134 AN: 10584

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48098 AN: 67886

Other (OTH) AF: 0.716 AC: 1511 AN: 2110

Alfa AF: 0.623 Hom.: 2136

Bravo AF: 0.712

Asia WGS AF: 0.886 AC: 3080 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.038
DANN	Benign	0.74
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1493829; hg19: chr12-74984758;