5-5341942-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:58997):

LOC101929200 (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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725525.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286753	ENST00000725525.1		n.156-22164G>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13187879;

hg19: chr5-5342055;