rs2414739

Variant names:

• chr15-61701935-G-A
• rs2414739
• ENST00000559590.3:n.102+13180C>T

Variant summary

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

The ENST00000559590.3(ENSG00000259675):​n.102+13180C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,004 control chromosomes in the GnomAD database, including 35,240 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 0.67 (35240 hom., cov: 32)
• Consequence: ENSG00000259675 ENST00000559590.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 45 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984782	XR_001751569.2	n.72+13180C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259675	ENST00000559590.3	n.102+13180C>T		intron_variant	Intron 1 of 1	3
ENSG00000259675	ENST00000662958.4	n.89+13180C>T		intron_variant	Intron 1 of 2
ENSG00000259675	ENST00000691967.3	n.91+13180C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102358 AN: 151886 Hom.: 35228 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.674 AC: 102420 AN: 152004 Hom.: 35240 Cov.: 32 AF XY: 0.672 AC XY: 49939 AN XY: 74290

African (AFR) AF: 0.529 AC: 21904 AN: 41432

American (AMR) AF: 0.743 AC: 11353 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2594 AN: 3470

East Asian (EAS) AF: 0.815 AC: 4211 AN: 5168

South Asian (SAS) AF: 0.684 AC: 3302 AN: 4826

European-Finnish (FIN) AF: 0.686 AC: 7243 AN: 10552

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.727 AC: 49408 AN: 67964

Other (OTH) AF: 0.731 AC: 1540 AN: 2108

Alfa AF: 0.720 Hom.: 181738

Bravo AF: 0.678

Asia WGS AF: 0.736 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.56
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2414739; hg19: chr15-61994134;