ENST00000543286.5:n.545+40258T>A

Variant names:

• chr15-93362604-T-A
• rs10520722
• ENST00000543286.5:n.545+40258T>A

Variant summary

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

The ENST00000543286.5(ENSG00000257060):​n.545+40258T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,982 control chromosomes in the GnomAD database, including 12,142 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 0.39 (12142 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000543286.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 0 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370982	XR_007064770.1	n.1161-10906T>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257060	ENST00000543286.5	n.545+40258T>A		intron_variant	Intron 2 of 3	2
ENSG00000257060	ENST00000553478.1	n.318+40258T>A		intron_variant	Intron 2 of 3	4
ENSG00000257060	ENST00000554105.6	n.423-10906T>A		intron_variant	Intron 2 of 5	4

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59542 AN: 151864 Hom.: 12131 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.392 AC: 59596 AN: 151982 Hom.: 12142 Cov.: 32 AF XY: 0.385 AC XY: 28591 AN XY: 74266

African (AFR) AF: 0.387 AC: 16043 AN: 41440

American (AMR) AF: 0.365 AC: 5577 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3470

East Asian (EAS) AF: 0.113 AC: 584 AN: 5178

South Asian (SAS) AF: 0.151 AC: 726 AN: 4820

European-Finnish (FIN) AF: 0.421 AC: 4432 AN: 10534

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29452 AN: 67948

Other (OTH) AF: 0.364 AC: 769 AN: 2112

Alfa AF: 0.421 Hom.: 1684

Bravo AF: 0.390

Asia WGS AF: 0.142 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.58
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs10520722; hg19: chr15-93905833;