chr13-32572915-C-T

Variant names:

• chr13-32572915-C-T
• rs718444

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 0.35 in 151,890 control chromosomes in the GnomAD database, including 9,485 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 (9485 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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: 0.350 AC: 53097 AN: 151772 Hom.: 9479 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.350 AC: 53147 AN: 151890 Hom.: 9485 Cov.: 31 AF XY: 0.351 AC XY: 26059 AN XY: 74238

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.337

Alfa AF: 0.368 Hom.: 2168

Bravo AF: 0.342

Asia WGS AF: 0.204 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718444; hg19: chr13-33147052;