15-36017564-C-T

Variant names:

• chr15-36017564-C-T
• rs2175271
• ENST00000561394.1:n.199+15629G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561394.1(ENSG00000259639):​n.199+15629G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 151,698 control chromosomes in the GnomAD database, including 5,600 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 0.22 (5600 hom., cov: 32)
• Consequence: ENSG00000259639 ENST00000561394.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

Genes affected

ENSG00000259639 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259639	ENST00000561394.1	n.199+15629G>A		intron_variant	Intron 3 of 4	3
ENSG00000259639	ENST00000650498.1	n.199+15629G>A		intron_variant	Intron 3 of 5
LINC02853	ENST00000668741.1	n.463-31538C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32582 AN: 151580 Hom.: 5563 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.0355

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0807

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.215 AC: 32687 AN: 151698 Hom.: 5600 Cov.: 32 AF XY: 0.216 AC XY: 15983 AN XY: 74154

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.0355

Gnomad4 NFE AF: 0.0807

Gnomad4 OTH AF: 0.203

Alfa AF: 0.153 Hom.: 757

Bravo AF: 0.250

Asia WGS AF: 0.311 AC: 1075 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2175271; hg19: chr15-36309765;