rs12372818

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 114 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.00763

Gnomad4 AMR AF: 0.0275

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0212

Gnomad4 FIN AF: 0.0431

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.0422

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12372818; hg19: chr13-47683125;