rs1459543

Variant names:

• chr4-117729190-G-A
• rs1459543
• ENST00000755294.1:n.275+20123C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-117729190-G-A
• chr4-117729190-G-T

Variant summary

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

The ENST00000755294.1(ENSG00000288921):​n.275+20123C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,990 control chromosomes in the GnomAD database, including 25,973 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 0.57 (25973 hom., cov: 32)
• Consequence: ENSG00000288921 ENST00000755294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 6 publications found

Genes affected

ENSG00000288921 (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 (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288921	ENST00000755294.1	n.275+20123C>T		intron_variant	Intron 3 of 5
ENSG00000288921	ENST00000755295.1	n.350+20024C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86361 AN: 151872 Hom.: 25927 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.569 AC: 86470 AN: 151990 Hom.: 25973 Cov.: 32 AF XY: 0.567 AC XY: 42125 AN XY: 74272

African (AFR) AF: 0.779 AC: 32311 AN: 41494

American (AMR) AF: 0.568 AC: 8667 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3468

East Asian (EAS) AF: 0.626 AC: 3219 AN: 5140

South Asian (SAS) AF: 0.458 AC: 2209 AN: 4818

European-Finnish (FIN) AF: 0.444 AC: 4678 AN: 10532

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31588 AN: 67964

Other (OTH) AF: 0.586 AC: 1239 AN: 2114

Alfa AF: 0.474 Hom.: 6077

Bravo AF: 0.593

Asia WGS AF: 0.548 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.45
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1459543; hg19: chr4-118650345;