13-38942490-G-T

Position:

• chr13-38942490-G-T

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 0.252 in 152,062 control chromosomes in the GnomAD database, including 5,577 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 0.25 (5577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38315 AN: 151942 Hom.: 5551 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.252 AC: 38393 AN: 152062 Hom.: 5577 Cov.: 32 AF XY: 0.252 AC XY: 18696 AN XY: 74328

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.236

Alfa AF: 0.199 Hom.: 6940

Bravo AF: 0.270

Asia WGS AF: 0.279 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315632; hg19: chr13-39516627;