ENST00000510592.2:n.58+14217A>T

Variant names:

• chr4-131961706-T-A
• rs189811
• ENST00000510592.2:n.58+14217A>T

Variant summary

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

The ENST00000510592.2(ENSG00000251555):​n.58+14217A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,382 control chromosomes in the GnomAD database, including 33,952 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 0.66 (33952 hom., cov: 29)
• Consequence: ENSG00000251555 ENST00000510592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 1 publications found

Genes affected

ENSG00000251555 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510592.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251555	ENST00000510592.2	TSL:5	n.58+14217A>T		intron	N/A
	ENSG00000251555	ENST00000812901.1		n.291+14217A>T		intron	N/A
	ENSG00000251555	ENST00000812902.1		n.267+14217A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.660 AC: 99763 AN: 151270 Hom.: 33937 Cov.: 29

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.659 AC: 99826 AN: 151382 Hom.: 33952 Cov.: 29 AF XY: 0.660 AC XY: 48816 AN XY: 73940

African (AFR) AF: 0.510 AC: 21069 AN: 41272

American (AMR) AF: 0.674 AC: 10251 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2225 AN: 3466

East Asian (EAS) AF: 0.384 AC: 1984 AN: 5164

South Asian (SAS) AF: 0.583 AC: 2801 AN: 4806

European-Finnish (FIN) AF: 0.808 AC: 8355 AN: 10338

Middle Eastern (MID) AF: 0.762 AC: 221 AN: 290

European-Non Finnish (NFE) AF: 0.749 AC: 50812 AN: 67830

Other (OTH) AF: 0.680 AC: 1426 AN: 2098

Alfa AF: 0.714 Hom.: 4789

Bravo AF: 0.643

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.073
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs189811; hg19: chr4-132882861;