ENST00000603530.6:n.*206G>C

Variant names:

• chr22-44570564-G-C
• ENST00000603530.6:n.207G>C

Variant summary

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

The ENST00000603530.6(LINC00207):​n.207G>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: 32)
• Consequence: LINC00207 ENST00000603530.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 0 publications found

Genes affected

LINC00207 (HGNC:37255): (long intergenic non-protein coding RNA 207)

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 (REVEL=0.011).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000603530.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00207	NR_028409.1		n.234G>C		non_coding_transcript_exon	Exon 3 of 5
	LINC00207	NR_028410.1		n.167G>C		non_coding_transcript_exon	Exon 2 of 4
	LINC00207	NR_028411.1		n.167G>C		non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00207	ENST00000603530.6	TSL:1	n.207G>C		non_coding_transcript_exon	Exon 2 of 4
	LINC00207	ENST00000605505.1	TSL:1	n.222G>C		non_coding_transcript_exon	Exon 3 of 5
	LINC00207	ENST00000334566.10	TSL:5	n.197G>C		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.76
DANN	Benign	0.58
PhyloP100		0.0050

Splicing

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

Other links and lift over

hg19: chr22-44966444;