rs10520120

Variant names:

• chr15-39148096-C-T
• rs10520120
• ENST00000558209.1:n.452-76488G>A

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.452-76488G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0245 in 152,246 control chromosomes in the GnomAD database, including 102 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 0.025 (102 hom., cov: 32)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 1 publications found

Genes affected

ENSG00000259345 (HGNC:):

LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558209.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259345	ENST00000558209.1	TSL:3	n.452-76488G>A		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.68-76488G>A		intron	N/A
	ENSG00000259345	ENST00000561058.5	TSL:4	n.45-76488G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0245 AC: 3729 AN: 152128 Hom.: 102 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0228

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.00207

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00595

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0245 AC: 3735 AN: 152246 Hom.: 102 Cov.: 32 AF XY: 0.0259 AC XY: 1928 AN XY: 74426

African (AFR) AF: 0.0412 AC: 1711 AN: 41552

American (AMR) AF: 0.0227 AC: 347 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3470

East Asian (EAS) AF: 0.120 AC: 618 AN: 5164

South Asian (SAS) AF: 0.106 AC: 511 AN: 4822

European-Finnish (FIN) AF: 0.00207 AC: 22 AN: 10610

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00594 AC: 404 AN: 68020

Other (OTH) AF: 0.0293 AC: 62 AN: 2114

Alfa AF: 0.0154 Hom.: 3

Bravo AF: 0.0254

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.66
PhyloP100		-0.011

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10520120;

hg19: chr15-39440297;