15-36874067-T-G

Variant names:

• chr15-36874067-T-G
• rs8037890
• ENST00000690156.1:n.385+2293A>C

Variant summary

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

The NR_024264.1(LOC145845):​n.687+2293A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 152,276 control chromosomes in the GnomAD database, including 209 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 0.049 (209 hom., cov: 32)
• Consequence: LOC145845 NR_024264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.22
• Publications: 4 publications found

Genes affected

ENSG00000259280 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_024264.1. 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
	LOC145845	NR_024264.1		n.687+2293A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259280	ENST00000690156.1		n.385+2293A>C		intron	N/A
	ENSG00000259280	ENST00000785414.1		n.587+2293A>C		intron	N/A
	ENSG00000259280	ENST00000785415.1		n.614-5228A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7432 AN: 152158 Hom.: 210 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0357

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0735

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0488 AC: 7431 AN: 152276 Hom.: 209 Cov.: 32 AF XY: 0.0492 AC XY: 3666 AN XY: 74466

African (AFR) AF: 0.0223 AC: 929 AN: 41572

American (AMR) AF: 0.0356 AC: 545 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3470

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5182

South Asian (SAS) AF: 0.112 AC: 541 AN: 4826

European-Finnish (FIN) AF: 0.0735 AC: 780 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0617 AC: 4196 AN: 68002

Other (OTH) AF: 0.0450 AC: 95 AN: 2110

Alfa AF: 0.0562 Hom.: 252

Bravo AF: 0.0416

Asia WGS AF: 0.0600 AC: 209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.1
DANN	Benign	0.42
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs8037890; hg19: chr15-37166268;