5-13214740-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 0.323 in 151,872 control chromosomes in the GnomAD database, including 8,449 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 0.32 (8449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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 = 0.385 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: 0.323 AC: 48965 AN: 151756 Hom.: 8444 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.323 AC: 48994 AN: 151872 Hom.: 8449 Cov.: 32 AF XY: 0.321 AC XY: 23858 AN XY: 74214

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.321

Alfa AF: 0.353 Hom.: 4835

Bravo AF: 0.319

Asia WGS AF: 0.240 AC: 834 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	0.92
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28207; hg19: chr5-13214852;