rs10520109

Positions:

• chr15-38810034-G-A
• chr15-38810034-G-T

Variant summary

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

The ENST00000644461.1(LINC02694):​n.97-12964G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02694	ENST00000644461.1	n.97-12964G>A		intron_variant, non_coding_transcript_variant
LINC02694	ENST00000645416.2	n.227-12964G>A		intron_variant, non_coding_transcript_variant
LINC02694	ENST00000646232.1	n.164-12964G>A		intron_variant, non_coding_transcript_variant
LINC02694	ENST00000647456.1	n.658+76713G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00999

Gnomad4 AMR AF: 0.0386

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.00851

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0214

Gnomad4 NFE AF: 0.0544

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0505 Hom.: 135

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520109; hg19: chr15-39102235;