chr13-37601607-G-T

Position:

• chr13-37601607-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 0.195 in 151,768 control chromosomes in the GnomAD database, including 3,641 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 0.19 (3641 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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: 0.195 AC: 29552 AN: 151650 Hom.: 3642 Cov.: 31

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0624

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.195 AC: 29552 AN: 151768 Hom.: 3641 Cov.: 31 AF XY: 0.195 AC XY: 14470 AN XY: 74128

Gnomad4 AFR AF: 0.0566

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0627

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.201

Alfa AF: 0.244 Hom.: 993

Bravo AF: 0.177

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.51
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17197908; hg19: chr13-38175744;