rs873294

chr13-110515070-G-A

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 0.188 in 152,196 control chromosomes in the GnomAD database, including 3,148 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 (3148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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: 0.188 AC: 28545 AN: 152076 Hom.: 3145 Cov.: 32

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.188 AC: 28577 AN: 152196 Hom.: 3148 Cov.: 32 AF XY: 0.195 AC XY: 14480 AN XY: 74402

Gnomad4 AFR AF: 0.0794

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.172

Alfa AF: 0.185 Hom.: 295

Bravo AF: 0.177

Asia WGS AF: 0.317 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs873294; hg19: chr13-111167417;