chr13-73154002-G-T

Position:

• chr13-73154002-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 0.461 in 152,048 control chromosomes in the GnomAD database, including 16,322 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 0.46 (16322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

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 = 0.517 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: 0.461 AC: 70103 AN: 151930 Hom.: 16306 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.461 AC: 70146 AN: 152048 Hom.: 16322 Cov.: 32 AF XY: 0.458 AC XY: 34031 AN XY: 74322

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.457

Alfa AF: 0.446 Hom.: 34654

Bravo AF: 0.464

Asia WGS AF: 0.455 AC: 1584 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	1.5
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9600079; hg19: chr13-73728139;