13-80242430-C-T

Variant names:

• chr13-80242430-C-T
• rs370787

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 0.356 in 152,068 control chromosomes in the GnomAD database, including 10,011 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 0.36 (10011 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 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: 0.356 AC: 54044 AN: 151950 Hom.: 9984 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.356 AC: 54120 AN: 152068 Hom.: 10011 Cov.: 33 AF XY: 0.359 AC XY: 26660 AN XY: 74364

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.352

Alfa AF: 0.324 Hom.: 16461

Bravo AF: 0.354

Asia WGS AF: 0.436 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs370787; hg19: chr13-80816565;