13-68413369-G-T

Variant names:

• chr13-68413369-G-T
• rs1411131

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 0.536 in 151,726 control chromosomes in the GnomAD database, including 23,467 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 0.54 (23467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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: 0.537 AC: 81365 AN: 151608 Hom.: 23464 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.536 AC: 81376 AN: 151726 Hom.: 23467 Cov.: 32 AF XY: 0.542 AC XY: 40147 AN XY: 74124

African (AFR) AF: 0.317 AC: 13123 AN: 41434

American (AMR) AF: 0.601 AC: 9166 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1909 AN: 3460

East Asian (EAS) AF: 0.791 AC: 4095 AN: 5176

South Asian (SAS) AF: 0.660 AC: 3186 AN: 4824

European-Finnish (FIN) AF: 0.618 AC: 6505 AN: 10532

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41697 AN: 67746

Other (OTH) AF: 0.560 AC: 1180 AN: 2106

Alfa AF: 0.561 Hom.: 3240

Bravo AF: 0.524

Asia WGS AF: 0.665 AC: 2303 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1411131; hg19: chr13-68987501;