chr5-5341942-C-A

Variant names:

• chr5-5341942-C-A
• rs13187879
• ENST00000725525.1:n.156-22164G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000725525.1(ENSG00000286753):​n.156-22164G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,204 control chromosomes in the GnomAD database, including 1,264 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 0.11 (1264 hom., cov: 32)
• Consequence: ENSG00000286753 ENST00000725525.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 0 publications found

Genes affected

ENSG00000286753 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929200	XR_001742583.3	n.818-22164G>T		intron_variant	Intron 2 of 5
LOC101929200	XR_007059119.1	n.818-22164G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286753	ENST00000725525.1	n.156-22164G>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17047 AN: 152086 Hom.: 1266 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0567

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.112 AC: 17051 AN: 152204 Hom.: 1264 Cov.: 32 AF XY: 0.117 AC XY: 8733 AN XY: 74410

African (AFR) AF: 0.0274 AC: 1137 AN: 41552

American (AMR) AF: 0.150 AC: 2285 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0567 AC: 197 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1307 AN: 5168

South Asian (SAS) AF: 0.115 AC: 556 AN: 4830

European-Finnish (FIN) AF: 0.189 AC: 1999 AN: 10582

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9191 AN: 68006

Other (OTH) AF: 0.0891 AC: 188 AN: 2110

Alfa AF: 0.124 Hom.: 639

Bravo AF: 0.105

Asia WGS AF: 0.159 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs13187879; hg19: chr5-5342055;