Variant chr3-176518922-C-CCACAGACGATGAGAAGAAACACATGATACCACTCAATCTGGCCCCTAACAGGCCACTTTTCACTTTACCAACATTCCAGTGGCTGCAGTAAATCACATGGTCAAGCTCAACATTTAGCAGGTGGGAAAATATACCTTCTTCAGTGGGTAGCACTGCAAAGTTGCATATCAAAAGACATGGATGCATAATTATAATACAAAAAGTCCATTGATGATTAAATGCAATGATTTAATCTACCTTAGCAGTATAATCAACTAAGAGGAGAGCAACATTTCCTATCTACATTTTCATACAAAATAGGGAAAGCAATCAGTTCTGCTCCTCATGGGATGAAGGGTAGGAACCT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The ENST00000652470.1(LINC01208):n.281-27516_281-27515insAGGTTCCTACCCTTCATCCCATGAGGAGCAGAACTGATTGCTTTCCCTATTTTGTATGAAAATGTAGATAGGAAATGTTGCTCTCCTCTTAGTTGATTATACTGCTAAGGTAGATTAAATCATTGCATTTAATCATCAATGGACTTTTTGTATTATAATTATGCATCCATGTCTTTTGATATGCAACTTTGCAGTGCTACCCACTGAAGAAGGTATATTTTCCCACCTGCTAAATGTTGAGCTTGACCATGTGATTTACTGCAGCCACTGGAATGTTGGTAAAGTGAAAAGTGGCCTGTTAGGGGCCAGATTGAGTGGTATCATGTGTTTCTTCTCATCGTCTGTG 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. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 32)

Consequence

LINC01208
ENST00000652470.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.640

Variant links:

Genes affected

LINC01208 (HGNC:49639): (long intergenic non-protein coding RNA 1208)

LINC01208 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 3-176518922-C-CCACAGACGATGAGAAGAAACACATGATACCACTCAATCTGGCCCCTAACAGGCCACTTTTCACTTTACCAACATTCCAGTGGCTGCAGTAAATCACATGGTCAAGCTCAACATTTAGCAGGTGGGAAAATATACCTTCTTCAGTGGGTAGCACTGCAAAGTTGCATATCAAAAGACATGGATGCATAATTATAATACAAAAAGTCCATTGATGATTAAATGCAATGATTTAATCTACCTTAGCAGTATAATCAACTAAGAGGAGAGCAACATTTCCTATCTACATTTTCATACAAAATAGGGAAAGCAATCAGTTCTGCTCCTCATGGGATGAAGGGTAGGAACCT is Benign according to our data. Variant chr3-176518922-C-CCACAGACGATGAGAAGAAACACATGATACCACTCAATCTGGCCCCTAACAGGCCACTTTTCACTTTACCAACATTCCAGTGGCTGCAGTAAATCACATGGTCAAGCTCAACATTTAGCAGGTGGGAAAATATACCTTCTTCAGTGGGTAGCACTGCAAAGTTGCATATCAAAAGACATGGATGCATAATTATAATACAAAAAGTCCATTGATGATTAAATGCAATGATTTAATCTACCTTAGCAGTATAATCAACTAAGAGGAGAGCAACATTTCCTATCTACATTTTCATACAAAATAGGGAAAGCAATCAGTTCTGCTCCTCATGGGATGAAGGGTAGGAACCT is described in ClinVar as [Likely_benign]. Clinvar id is 988888.Status of the report is criteria_provided_single_submitter, 1 stars.

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
LINC01208	ENST00000652470.1 linkuse as main transcript	n.281-27516_281-27515insAGGTTCCTACCCTTCATCCCATGAGGAGCAGAACTGATTGCTTTCCCTATTTTGTATGAAAATGTAGATAGGAAATGTTGCTCTCCTCTTAGTTGATTATACTGCTAAGGTAGATTAAATCATTGCATTTAATCATCAATGGACTTTTTGTATTATAATTATGCATCCATGTCTTTTGATATGCAACTTTGCAGTGCTACCCACTGAAGAAGGTATATTTTCCCACCTGCTAAATGTTGAGCTTGACCATGTGATTTACTGCAGCCACTGGAATGTTGGTAAAGTGAAAAGTGGCCTGTTAGGGGCCAGATTGAGTGGTATCATGTGTTTCTTCTCATCGTCTGTG		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

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Developmental cataract

Benign:1

Likely benign, criteria provided, single submitter

research

Dept. Genetics and Cancer, Menzies Institute for Medical Research, University of Tasmania

Dec 01, 2020

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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

No publications associated with this variant yet.