rs1572372

chr13-20265865-C-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 0.354 in 152,022 control chromosomes in the GnomAD database, including 10,253 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 0.35 (10253 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.832

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 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: 0.354 AC: 53768 AN: 151904 Hom.: 10242 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.354 AC: 53814 AN: 152022 Hom.: 10253 Cov.: 32 AF XY: 0.358 AC XY: 26567 AN XY: 74294

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.366

Alfa AF: 0.400 Hom.: 5922

Bravo AF: 0.338

Asia WGS AF: 0.446 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	8.8
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1572372; hg19: chr13-20840004;