rs10520106

Variant names:

• chr15-38807948-G-A
• rs10520106
• ENST00000644461.1:n.97-15050G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-38807948-G-A
• chr15-38807948-G-T

Variant summary

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

The ENST00000644461.1(LINC02694):​n.97-15050G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0498 in 152,240 control chromosomes in the GnomAD database, including 625 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 0.050 (625 hom., cov: 32)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 2 publications found

Genes affected

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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
LINC02694	ENST00000644461.1	n.97-15050G>A		intron_variant	Intron 1 of 4
LINC02694	ENST00000645416.2	n.227-15050G>A		intron_variant	Intron 2 of 2
LINC02694	ENST00000645994.2	n.342-15050G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0497 AC: 7560 AN: 152122 Hom.: 626 Cov.: 32

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0179

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0498 AC: 7575 AN: 152240 Hom.: 625 Cov.: 32 AF XY: 0.0543 AC XY: 4044 AN XY: 74442

African (AFR) AF: 0.0353 AC: 1467 AN: 41560

American (AMR) AF: 0.135 AC: 2062 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1748 AN: 5176

South Asian (SAS) AF: 0.130 AC: 626 AN: 4824

European-Finnish (FIN) AF: 0.0291 AC: 309 AN: 10620

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0179 AC: 1217 AN: 67998

Other (OTH) AF: 0.0569 AC: 120 AN: 2108

Alfa AF: 0.0471 Hom.: 66

Bravo AF: 0.0555

Asia WGS AF: 0.251 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.38
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10520106; hg19: chr15-39100149;