13-105547179-G-T

Variant names:

• chr13-105547179-G-T
• rs2052383

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 0.707 in 151,924 control chromosomes in the GnomAD database, including 39,897 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 0.71 (39897 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.834 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: 0.707 AC: 107358 AN: 151808 Hom.: 39885 Cov.: 30

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.707 AC: 107407 AN: 151924 Hom.: 39897 Cov.: 30 AF XY: 0.711 AC XY: 52784 AN XY: 74226

African (AFR) AF: 0.463 AC: 19149 AN: 41370

American (AMR) AF: 0.846 AC: 12927 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2920 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3154 AN: 5138

South Asian (SAS) AF: 0.703 AC: 3382 AN: 4814

European-Finnish (FIN) AF: 0.808 AC: 8539 AN: 10564

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

European-Non Finnish (NFE) AF: 0.806 AC: 54789 AN: 67968

Other (OTH) AF: 0.749 AC: 1582 AN: 2112

Alfa AF: 0.776 Hom.: 68354

Bravo AF: 0.702

Asia WGS AF: 0.658 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.074
DANN	Benign	0.59
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2052383; hg19: chr13-106199528;