rs10834691

Variant names:

• chr11-25468936-G-A
• rs10834691
• ENST00000812472.1:n.124+15274G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-25468936-G-A
• chr11-25468936-G-C
• chr11-25468936-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000812472.1(ENSG00000305694):​n.124+15274G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ENSG00000305694 ENST00000812472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950
• Publications: 2 publications found

Genes affected

ENSG00000305694 (HGNC:):

LINC02699 (HGNC:54213): (long intergenic non-protein coding RNA 2699)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02699	NR_183693.1	n.64-1569G>A		intron_variant	Intron 1 of 5
LINC02699	NR_183694.1	n.63+15274G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305694	ENST00000812472.1	n.124+15274G>A		intron_variant	Intron 1 of 1
ENSG00000305694	ENST00000812473.1	n.86-1569G>A		intron_variant	Intron 1 of 3
ENSG00000305694	ENST00000812474.1	n.65-1569G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 4010

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.20
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs10834691; hg19: chr11-25490482;