rs1925058

Variant names:

• chr13-55008992-G-A
• rs1925058

Your query was ambiguous. Multiple possible variants found:

• chr13-55008992-G-A
• chr13-55008992-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.725

Alfa AF: 0.697 Hom.: 14846

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1925058; hg19: chr13-55583127;