4-141256726-A-T

Variant names:

• chr4-141256726-A-T
• rs1541964
• ENST00000514347.1:n.447-15397T>A

Variant summary

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

The ENST00000514347.1(ENSG00000248747):​n.447-15397T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,088 control chromosomes in the GnomAD database, including 39,727 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 0.71 (39727 hom., cov: 32)
• Consequence: ENSG00000248747 ENST00000514347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 2 publications found

Genes affected

ENSG00000248747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514347.1. 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
	ENSG00000248747	ENST00000514347.1	TSL:3	n.447-15397T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107527 AN: 151970 Hom.: 39671 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.708 AC: 107643 AN: 152088 Hom.: 39727 Cov.: 32 AF XY: 0.703 AC XY: 52220 AN XY: 74330

African (AFR) AF: 0.923 AC: 38351 AN: 41528

American (AMR) AF: 0.644 AC: 9846 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2207 AN: 3470

East Asian (EAS) AF: 0.781 AC: 4039 AN: 5174

South Asian (SAS) AF: 0.762 AC: 3666 AN: 4814

European-Finnish (FIN) AF: 0.533 AC: 5616 AN: 10540

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41579 AN: 67952

Other (OTH) AF: 0.704 AC: 1489 AN: 2114

Alfa AF: 0.649 Hom.: 3886

Bravo AF: 0.725

Asia WGS AF: 0.753 AC: 2610 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.32
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1541964; hg19: chr4-142177880;