5-132017592-C-T

Variant names:

• chr5-132017592-C-T
• rs3914025

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 0.514 in 151,970 control chromosomes in the GnomAD database, including 20,333 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 0.51 (20333 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 5 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 (AMR) 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: 0.514 AC: 78038 AN: 151852 Hom.: 20314 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.514 AC: 78107 AN: 151970 Hom.: 20333 Cov.: 33 AF XY: 0.506 AC XY: 37609 AN XY: 74256

African (AFR) AF: 0.548 AC: 22724 AN: 41438

American (AMR) AF: 0.553 AC: 8446 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1689 AN: 3466

East Asian (EAS) AF: 0.542 AC: 2801 AN: 5172

South Asian (SAS) AF: 0.311 AC: 1496 AN: 4812

European-Finnish (FIN) AF: 0.433 AC: 4553 AN: 10514

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34648 AN: 67972

Other (OTH) AF: 0.530 AC: 1117 AN: 2106

Alfa AF: 0.503 Hom.: 2688

Bravo AF: 0.533

Asia WGS AF: 0.445 AC: 1548 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	7.4
DANN	Benign	0.67
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs3914025; hg19: chr5-131353285;