rs1572372

Variant names:

• chr13-20265865-C-T
• rs1572372

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.207 AC: 8590 AN: 41466

American (AMR) AF: 0.363 AC: 5549 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1237 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1878 AN: 5180

South Asian (SAS) AF: 0.413 AC: 1987 AN: 4814

European-Finnish (FIN) AF: 0.433 AC: 4557 AN: 10532

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28767 AN: 67968

Other (OTH) AF: 0.366 AC: 769 AN: 2100

Alfa AF: 0.391 Hom.: 22505

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
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs1572372; hg19: chr13-20840004;