rs12324805

Variant names:

• chr15-82059859-C-A
• rs12324805

Your query was ambiguous. Multiple possible variants found:

• chr15-82059859-C-A
• chr15-82059859-C-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 0.729 in 151,866 control chromosomes in the GnomAD database, including 40,913 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 0.73 (40913 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 18 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.855 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: 0.729 AC: 110588 AN: 151748 Hom.: 40876 Cov.: 31

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.729 AC: 110682 AN: 151866 Hom.: 40913 Cov.: 31 AF XY: 0.726 AC XY: 53893 AN XY: 74208

African (AFR) AF: 0.863 AC: 35725 AN: 41400

American (AMR) AF: 0.705 AC: 10744 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2568 AN: 3472

East Asian (EAS) AF: 0.649 AC: 3329 AN: 5130

South Asian (SAS) AF: 0.524 AC: 2520 AN: 4810

European-Finnish (FIN) AF: 0.698 AC: 7348 AN: 10522

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46238 AN: 67968

Other (OTH) AF: 0.711 AC: 1499 AN: 2108

Alfa AF: 0.694 Hom.: 141157

Bravo AF: 0.732

Asia WGS AF: 0.563 AC: 1961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs12324805; hg19: chr15-82352200;