13-72152782-C-T

Variant names:

• chr13-72152782-C-T
• rs1421280

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 0.735 in 151,938 control chromosomes in the GnomAD database, including 41,531 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 0.73 (41531 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.776 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: 0.735 AC: 111526 AN: 151818 Hom.: 41497 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.735 AC: 111609 AN: 151938 Hom.: 41531 Cov.: 31 AF XY: 0.726 AC XY: 53917 AN XY: 74248

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.727

Alfa AF: 0.755 Hom.: 5842

Bravo AF: 0.723

Asia WGS AF: 0.606 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1421280; hg19: chr13-72726920;