rs12372818

Variant names:

• chr13-47108990-G-A
• rs12372818

Your query was ambiguous. Multiple possible variants found:

• chr13-47108990-G-A
• chr13-47108990-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0321 in 152,254 control chromosomes in the GnomAD database, including 114 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 0.032 (114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0321 (4886/152254) while in subpopulation NFE AF = 0.0487 (3311/68022). AF 95% confidence interval is 0.0473. There are 114 homozygotes in GnomAd4. There are 2323 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 114 gene

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: 0.0321 AC: 4886 AN: 152136 Hom.: 114 Cov.: 32

Gnomad AFR AF: 0.00765

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0274

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0212

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0321 AC: 4886 AN: 152254 Hom.: 114 Cov.: 32 AF XY: 0.0312 AC XY: 2323 AN XY: 74446

African (AFR) AF: 0.00763 AC: 317 AN: 41548

American (AMR) AF: 0.0275 AC: 420 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0499 AC: 173 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.0212 AC: 102 AN: 4818

European-Finnish (FIN) AF: 0.0431 AC: 457 AN: 10610

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0487 AC: 3311 AN: 68022

Other (OTH) AF: 0.0422 AC: 89 AN: 2110

Alfa AF: 0.0204 Hom.: 6

Bravo AF: 0.0303

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.74
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs12372818; hg19: chr13-47683125;