13-105063667-A-G

Variant names:

• chr13-105063667-A-G
• rs12428682

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 0.666 in 152,122 control chromosomes in the GnomAD database, including 34,359 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 0.67 (34359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• 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).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101231 AN: 152004 Hom.: 34331 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.666 AC: 101300 AN: 152122 Hom.: 34359 Cov.: 32 AF XY: 0.670 AC XY: 49850 AN XY: 74390

African (AFR) AF: 0.760 AC: 31516 AN: 41486

American (AMR) AF: 0.534 AC: 8160 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2179 AN: 3470

East Asian (EAS) AF: 0.933 AC: 4833 AN: 5180

South Asian (SAS) AF: 0.768 AC: 3709 AN: 4830

European-Finnish (FIN) AF: 0.678 AC: 7177 AN: 10582

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41436 AN: 67966

Other (OTH) AF: 0.655 AC: 1386 AN: 2116

Alfa AF: 0.628 Hom.: 90707

Bravo AF: 0.658

Asia WGS AF: 0.827 AC: 2878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs12428682; hg19: chr13-105716018;