ENST00000561054.2:n.314-746G>T

Variant names:

• chr15-37367848-C-A
• rs587847
• ENST00000561054.2:n.314-746G>T

Variant summary

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

The ENST00000561054.2(ENSG00000259434):​n.314-746G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,986 control chromosomes in the GnomAD database, including 36,467 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 0.68 (36467 hom., cov: 31)
• Consequence: ENSG00000259434 ENST00000561054.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 8 publications found

Genes affected

ENSG00000259434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561054.2. 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
	ENSG00000259434	ENST00000561054.2	TSL:3	n.314-746G>T		intron	N/A
	ENSG00000259434	ENST00000663330.1		n.242-746G>T		intron	N/A
	ENSG00000259434	ENST00000669587.1		n.388-746G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104007 AN: 151868 Hom.: 36428 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.685 AC: 104102 AN: 151986 Hom.: 36467 Cov.: 31 AF XY: 0.681 AC XY: 50602 AN XY: 74280

African (AFR) AF: 0.839 AC: 34800 AN: 41476

American (AMR) AF: 0.657 AC: 10018 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1879 AN: 3468

East Asian (EAS) AF: 0.772 AC: 3983 AN: 5158

South Asian (SAS) AF: 0.424 AC: 2037 AN: 4804

European-Finnish (FIN) AF: 0.668 AC: 7038 AN: 10540

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42246 AN: 67972

Other (OTH) AF: 0.663 AC: 1402 AN: 2114

Alfa AF: 0.646 Hom.: 21751

Bravo AF: 0.699

Asia WGS AF: 0.628 AC: 2177 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs587847; hg19: chr15-37660049;