chr18-56025735-C-T

Variant names:

• chr18-56025735-C-T
• rs2646965
• ENST00000666716.1:n.2714C>T

Variant summary

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

The ENST00000666716.1(LINC01905):​n.2714C>T variant causes a non coding transcript exon 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: LINC01905 ENST00000666716.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 0 publications found

Genes affected

LINC01905 (HGNC:52724): (long intergenic non-protein coding RNA 1905)

LINC03092 (HGNC:56721): (long intergenic non-protein coding RNA 3092)

LINC01539 (HGNC:51307): (long intergenic non-protein coding RNA 1539)

LINC03069 (HGNC:56641): (long intergenic non-protein coding RNA 3069)

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=-0.52).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03092	XR_001753453.3	n.2454C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC03092	XR_001753454.2	n.4833C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC03069	NR_148972.1	n.2212-340G>A		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01905	ENST00000666716.1	n.2714C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC01539	ENST00000382897.2	n.2212-340G>A		intron_variant	Intron 7 of 8	2
LINC01539	ENST00000650203.1	n.1463-340G>A		intron_variant	Intron 3 of 4

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	12
DANN	Benign	0.64
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2646965; hg19: chr18-53692966;