13-75027216-C-T

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 0.479 in 151,852 control chromosomes in the GnomAD database, including 19,167 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 0.48 (19167 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72717 AN: 151734 Hom.: 19170 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.479 AC: 72716 AN: 151852 Hom.: 19167 Cov.: 31 AF XY: 0.478 AC XY: 35475 AN XY: 74194

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.502

Alfa AF: 0.540 Hom.: 11218

Bravo AF: 0.469

Asia WGS AF: 0.489 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	6.9
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417549; hg19: chr13-75601353;