Variant chr15-38985058-A-AGAG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000560484.1(ENSG00000259345):n.174-10824_174-10823insCTC variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

ENST00000560484.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.370

Variant links:

Genes affected

(HGNC:):

links:

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

LINC02694 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC105370777	XR_007064586.1 linkuse as main transcript	n.1446-10824_1446-10823insCTC	intron_variant, non_coding_transcript_variant
LOC105370777	XR_007064587.1 linkuse as main transcript	n.1446-10824_1446-10823insCTC	intron_variant, non_coding_transcript_variant
LOC105370777	XR_007064588.1 linkuse as main transcript	n.624-10824_624-10823insCTC	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000560484.1 linkuse as main transcript	n.174-10824_174-10823insCTC		intron_variant, non_coding_transcript_variant		4
LINC02694	ENST00000644461.1 linkuse as main transcript	n.158+161999_158+162000insGAG		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.