chr13-55008992-G-A

Variant names:

• chr13-55008992-G-A
• rs1925058

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 0.697 in 151,726 control chromosomes in the GnomAD database, including 37,075 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 0.70 (37075 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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: 0.697 AC: 105601 AN: 151606 Hom.: 37047 Cov.: 31

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.697 AC: 105682 AN: 151726 Hom.: 37075 Cov.: 31 AF XY: 0.702 AC XY: 52053 AN XY: 74140

African (AFR) AF: 0.634 AC: 26255 AN: 41404

American (AMR) AF: 0.684 AC: 10405 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2623 AN: 3466

East Asian (EAS) AF: 0.892 AC: 4582 AN: 5138

South Asian (SAS) AF: 0.802 AC: 3854 AN: 4808

European-Finnish (FIN) AF: 0.753 AC: 7901 AN: 10490

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47669 AN: 67896

Other (OTH) AF: 0.725 AC: 1521 AN: 2098

Alfa AF: 0.697 Hom.: 16748

Bravo AF: 0.689

Asia WGS AF: 0.834 AC: 2902 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	0.21
DANN	Benign	0.67
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1925058; hg19: chr13-55583127;