rs10520109

Variant names:

• chr15-38810034-G-A
• rs10520109
• ENST00000644461.1:n.97-12964G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-38810034-G-A
• chr15-38810034-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.97-12964G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 152,142 control chromosomes in the GnomAD database, including 202 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 0.040 (202 hom., cov: 32)
• Consequence: LINC02694 ENST00000644461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 0 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 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.97-12964G>A		intron_variant	Intron 1 of 4
LINC02694	ENST00000645416.2	n.227-12964G>A		intron_variant	Intron 2 of 2
LINC02694	ENST00000645994.2	n.342-12964G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0397 AC: 6033 AN: 152024 Hom.: 201 Cov.: 32

Gnomad AFR AF: 0.0100

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.00849

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0214

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0544

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0396 AC: 6031 AN: 152142 Hom.: 202 Cov.: 32 AF XY: 0.0398 AC XY: 2963 AN XY: 74384

African (AFR) AF: 0.00999 AC: 415 AN: 41524

American (AMR) AF: 0.0386 AC: 590 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3472

East Asian (EAS) AF: 0.00851 AC: 44 AN: 5170

South Asian (SAS) AF: 0.121 AC: 581 AN: 4814

European-Finnish (FIN) AF: 0.0214 AC: 227 AN: 10592

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0544 AC: 3700 AN: 67984

Other (OTH) AF: 0.0378 AC: 80 AN: 2114

Alfa AF: 0.0514 Hom.: 148

Bravo AF: 0.0368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.39
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs10520109; hg19: chr15-39102235;