ENST00000693076.1:n.1626G>C

Variant names:

• chr14-77031632-C-G
• rs183266
• ENST00000693076.1:n.1626G>C

Variant summary

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

The ENST00000693076.1(ENSG00000289347):​n.1626G>C 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: 31)
• Consequence: ENSG00000289347 ENST00000693076.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 11 publications found

Genes affected

ENSG00000289347 (HGNC:):

LINC02289 (HGNC:53205): (long intergenic non-protein coding RNA 2289)

LINC02288 (HGNC:27505): (long intergenic non-protein coding RNA 2288)

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=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000693076.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105370579	NR_169510.1		n.1951G>C		non_coding_transcript_exon	Exon 2 of 2
	LOC107984638	NR_190001.1		n.*60C>G		downstream_gene	N/A
	LOC107984638	NR_190002.1		n.*60C>G		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289347	ENST00000693076.1		n.1626G>C		non_coding_transcript_exon	Exon 2 of 2
	LINC02289	ENST00000716908.1		n.304+9422G>C		intron	N/A
	LINC02288	ENST00000793445.1		n.62+3821C>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 145394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.19
DANN	Benign	0.24
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs183266;

hg19: chr14-77497975;