15-61578744-C-T

Variant names:

• chr15-61578744-C-T
• rs12592967
• ENST00000559783.2:n.123+11172G>A

Variant summary

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

The ENST00000559783.2(ENSG00000259675):​n.123+11172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,908 control chromosomes in the GnomAD database, including 15,748 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 0.44 (15748 hom., cov: 31)
• Consequence: ENSG00000259675 ENST00000559783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 9 publications found

Genes affected

ENSG00000259675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559783.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259675	ENST00000559783.2	TSL:3	n.123+11172G>A		intron	N/A
	ENSG00000259675	ENST00000748013.1		n.346+11172G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66375 AN: 151790 Hom.: 15748 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.437 AC: 66385 AN: 151908 Hom.: 15748 Cov.: 31 AF XY: 0.434 AC XY: 32220 AN XY: 74204

African (AFR) AF: 0.255 AC: 10572 AN: 41408

American (AMR) AF: 0.433 AC: 6618 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1944 AN: 3466

East Asian (EAS) AF: 0.291 AC: 1497 AN: 5148

South Asian (SAS) AF: 0.451 AC: 2167 AN: 4810

European-Finnish (FIN) AF: 0.474 AC: 4996 AN: 10538

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37087 AN: 67950

Other (OTH) AF: 0.459 AC: 965 AN: 2104

Alfa AF: 0.487 Hom.: 33912

Bravo AF: 0.421

Asia WGS AF: 0.367 AC: 1277 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.47
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs12592967; hg19: chr15-61870943;