rs1542725

Variant names:

• chr4-144567182-C-T
• rs1542725
• ENST00000649263.1:n.328-151204G>A

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-151204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,020 control chromosomes in the GnomAD database, including 9,479 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 (9479 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 12 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. 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
	ENSG00000285713	ENST00000649263.1		n.328-151204G>A		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.223-151204G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48420 AN: 151902 Hom.: 9470 Cov.: 32

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.319 AC: 48432 AN: 152020 Hom.: 9479 Cov.: 32 AF XY: 0.326 AC XY: 24199 AN XY: 74284

African (AFR) AF: 0.0948 AC: 3931 AN: 41484

American (AMR) AF: 0.303 AC: 4627 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3464

East Asian (EAS) AF: 0.300 AC: 1551 AN: 5166

South Asian (SAS) AF: 0.492 AC: 2367 AN: 4812

European-Finnish (FIN) AF: 0.536 AC: 5654 AN: 10540

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28017 AN: 67974

Other (OTH) AF: 0.304 AC: 642 AN: 2110

Alfa AF: 0.379 Hom.: 1566

Bravo AF: 0.284

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.5
DANN	Benign	0.57
PhyloP100		-0.29

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: rs1542725;

hg19: chr4-145488334;