15-87434245-A-G

Variant names:

• chr15-87434245-A-G
• rs2679073
• ENST00000560439.1:n.279-1012T>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000560439.1(ENSG00000259560):​n.279-1012T>C variant causes a intron change. The variant allele was found at a frequency of 0.0393 in 152,268 control chromosomes in the GnomAD database, including 194 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 0.039 (194 hom., cov: 33)
• Consequence: ENSG00000259560 ENST00000560439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.21
• Publications: 8 publications found

Genes affected

ENSG00000259560 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724465	NR_187944.1	n.143-1012T>C		intron_variant	Intron 2 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259560	ENST00000560439.1	n.279-1012T>C		intron_variant	Intron 4 of 5	3
ENSG00000259560	ENST00000656130.2	n.263-1012T>C		intron_variant	Intron 3 of 4
ENSG00000259560	ENST00000665121.1	n.113-1012T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0393 AC: 5976 AN: 152150 Hom.: 191 Cov.: 33

Gnomad AFR AF: 0.00897

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.0300

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0715

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0393 AC: 5986 AN: 152268 Hom.: 194 Cov.: 33 AF XY: 0.0423 AC XY: 3151 AN XY: 74428

African (AFR) AF: 0.00895 AC: 372 AN: 41574

American (AMR) AF: 0.0990 AC: 1510 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3470

East Asian (EAS) AF: 0.0303 AC: 157 AN: 5186

South Asian (SAS) AF: 0.0424 AC: 205 AN: 4832

European-Finnish (FIN) AF: 0.0715 AC: 759 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0384 AC: 2612 AN: 68028

Other (OTH) AF: 0.0345 AC: 73 AN: 2114

Alfa AF: 0.0376 Hom.: 25

Bravo AF: 0.0376

Asia WGS AF: 0.0350 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Benign	17
DANN	Benign	0.88
PhyloP100		5.2
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2679073; hg19: chr15-87977476;