13-38465795-T-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 0.546 in 151,808 control chromosomes in the GnomAD database, including 23,967 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 0.55 (23967 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.547 AC: 82898 AN: 151688 Hom.: 23962 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.546 AC: 82916 AN: 151808 Hom.: 23967 Cov.: 31 AF XY: 0.545 AC XY: 40440 AN XY: 74184

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.529

Alfa AF: 0.613 Hom.: 3646

Bravo AF: 0.524

Asia WGS AF: 0.357 AC: 1232 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.2
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs980285; hg19: chr13-39039932; COSMIC: COSV69347495;