13-73237742-A-T

Variant names:

• chr13-73237742-A-T
• rs9600103

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 0.321 in 146,658 control chromosomes in the GnomAD database, including 8,358 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 0.32 (8358 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 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: 0.321 AC: 47047 AN: 146598 Hom.: 8352 Cov.: 27

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.375

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.321 AC: 47081 AN: 146658 Hom.: 8358 Cov.: 27 AF XY: 0.314 AC XY: 22374 AN XY: 71168

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.0499

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.331

Alfa AF: 0.135 Hom.: 238

Bravo AF: 0.329

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9600103; hg19: chr13-73811879;