5-5361356-G-T

Variant names:

• chr5-5361356-G-T
• rs2964459
• ENST00000725525.1:n.156-41578C>A

Variant summary

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

The ENST00000725525.1(ENSG00000286753):​n.156-41578C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,064 control chromosomes in the GnomAD database, including 15,156 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 0.43 (15156 hom., cov: 33)
• Consequence: ENSG00000286753 ENST00000725525.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 4 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286753	ENST00000725525.1		n.156-41578C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65171 AN: 151944 Hom.: 15162 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.429 AC: 65166 AN: 152064 Hom.: 15156 Cov.: 33 AF XY: 0.424 AC XY: 31521 AN XY: 74320

African (AFR) AF: 0.239 AC: 9928 AN: 41490

American (AMR) AF: 0.475 AC: 7253 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1861 AN: 3468

East Asian (EAS) AF: 0.342 AC: 1764 AN: 5164

South Asian (SAS) AF: 0.397 AC: 1910 AN: 4812

European-Finnish (FIN) AF: 0.479 AC: 5056 AN: 10548

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35763 AN: 67986

Other (OTH) AF: 0.482 AC: 1017 AN: 2110

Alfa AF: 0.489 Hom.: 47146

Bravo AF: 0.421

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.39
DANN	Benign	0.54
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs2964459; hg19: chr5-5361469;