15-36057645-T-C

Variant names:

• chr15-36057645-T-C
• rs1898036
• ENST00000561394.2:n.137-24390A>G

Variant summary

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

The ENST00000561394.2(ENSG00000259639):​n.137-24390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0877 in 152,242 control chromosomes in the GnomAD database, including 852 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 0.088 (852 hom., cov: 32)
• Consequence: ENSG00000259639 ENST00000561394.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 7 publications found

Genes affected

ENSG00000259639 (HGNC:):

LINC02853 (HGNC:54390): (long intergenic non-protein coding RNA 2853)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561394.2. 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
	ENSG00000259639	ENST00000561394.2	TSL:3	n.137-24390A>G		intron	N/A
	ENSG00000259639	ENST00000650498.1		n.137-24390A>G		intron	N/A
	ENSG00000259639	ENST00000820117.1		n.134-24390A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0878 AC: 13357 AN: 152124 Hom.: 850 Cov.: 32

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0877 AC: 13355 AN: 152242 Hom.: 852 Cov.: 32 AF XY: 0.0932 AC XY: 6939 AN XY: 74414

African (AFR) AF: 0.0237 AC: 984 AN: 41560

American (AMR) AF: 0.0592 AC: 905 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0374 AC: 130 AN: 3472

East Asian (EAS) AF: 0.146 AC: 758 AN: 5182

South Asian (SAS) AF: 0.173 AC: 834 AN: 4822

European-Finnish (FIN) AF: 0.236 AC: 2497 AN: 10564

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

European-Non Finnish (NFE) AF: 0.104 AC: 7045 AN: 68026

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0935 Hom.: 2437

Bravo AF: 0.0701

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.4
DANN	Benign	0.87
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1898036; hg19: chr15-36349846;