13-68413369-G-T

Variant names:

• chr13-68413369-G-T
• rs1411131

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 0.536 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.537 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

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.560

Alfa AF: 0.571 Hom.: 3208

Bravo AF: 0.524

Asia WGS AF: 0.665 AC: 2303 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1411131; hg19: chr13-68987501;