13-105420521-A-G

Variant names:

• chr13-105420521-A-G
• rs2025522

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 0.686 in 152,056 control chromosomes in the GnomAD database, including 35,915 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 0.69 (35915 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.773 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: 0.686 AC: 104244 AN: 151938 Hom.: 35906 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.686 AC: 104300 AN: 152056 Hom.: 35915 Cov.: 32 AF XY: 0.682 AC XY: 50657 AN XY: 74318

African (AFR) AF: 0.634 AC: 26310 AN: 41472

American (AMR) AF: 0.721 AC: 11007 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2445 AN: 3472

East Asian (EAS) AF: 0.793 AC: 4105 AN: 5174

South Asian (SAS) AF: 0.696 AC: 3357 AN: 4826

European-Finnish (FIN) AF: 0.572 AC: 6040 AN: 10552

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.717 AC: 48751 AN: 67974

Other (OTH) AF: 0.692 AC: 1462 AN: 2114

Alfa AF: 0.708 Hom.: 21224

Bravo AF: 0.693

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.57
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2025522; hg19: chr13-106072870;