13-72152782-C-T

Variant names:

• chr13-72152782-C-T
• rs1421280

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 0.735 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.750 AC: 31092 AN: 41460

American (AMR) AF: 0.623 AC: 9495 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2646 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2039 AN: 5146

South Asian (SAS) AF: 0.687 AC: 3304 AN: 4806

European-Finnish (FIN) AF: 0.722 AC: 7599 AN: 10528

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53082 AN: 67958

Other (OTH) AF: 0.727 AC: 1536 AN: 2114

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
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs1421280; hg19: chr13-72726920;