chr13-73250879-A-G

Position:

• chr13-73250879-A-G

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 0.474 in 151,938 control chromosomes in the GnomAD database, including 17,279 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 0.47 (17279 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 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: 0.474 AC: 71949 AN: 151820 Hom.: 17258 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.474 AC: 72008 AN: 151938 Hom.: 17279 Cov.: 31 AF XY: 0.476 AC XY: 35311 AN XY: 74250

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.479

Alfa AF: 0.467 Hom.: 10337

Bravo AF: 0.485

Asia WGS AF: 0.612 AC: 2132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
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: rs1023102; hg19: chr13-73825016;