13-105065312-A-G

Variant names:

• chr13-105065312-A-G
• rs7139453

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 151,848 control chromosomes in the GnomAD database, including 34,280 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 (34280 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.666 AC: 101031 AN: 151730 Hom.: 34252 Cov.: 30

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.787

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: 101100 AN: 151848 Hom.: 34280 Cov.: 30 AF XY: 0.670 AC XY: 49696 AN XY: 74176

African (AFR) AF: 0.760 AC: 31461 AN: 41416

American (AMR) AF: 0.534 AC: 8139 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2177 AN: 3466

East Asian (EAS) AF: 0.933 AC: 4798 AN: 5144

South Asian (SAS) AF: 0.768 AC: 3698 AN: 4814

European-Finnish (FIN) AF: 0.678 AC: 7110 AN: 10490

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

European-Non Finnish (NFE) AF: 0.610 AC: 41429 AN: 67956

Other (OTH) AF: 0.655 AC: 1383 AN: 2112

Alfa AF: 0.629 Hom.: 15923

Bravo AF: 0.658

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.50
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs7139453; hg19: chr13-105717663;