13-25085044-G-T

Variant names:

• chr13-25085044-G-T
• rs1013478

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 0.112 in 152,140 control chromosomes in the GnomAD database, including 1,467 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 0.11 (1467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16978 AN: 152022 Hom.: 1469 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0239

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.112 AC: 16984 AN: 152140 Hom.: 1467 Cov.: 32 AF XY: 0.109 AC XY: 8123 AN XY: 74372

African (AFR) AF: 0.233 AC: 9667 AN: 41476

American (AMR) AF: 0.138 AC: 2112 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3472

East Asian (EAS) AF: 0.0629 AC: 326 AN: 5184

South Asian (SAS) AF: 0.0197 AC: 95 AN: 4820

European-Finnish (FIN) AF: 0.0239 AC: 253 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0573 AC: 3899 AN: 67992

Other (OTH) AF: 0.111 AC: 235 AN: 2108

Alfa AF: 0.0749 Hom.: 1378

Bravo AF: 0.127

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.65
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1013478; hg19: chr13-25659182;