ENST00000603530.6:n.207G>T

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000603530.6(LINC00207):​n.207G>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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.017).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00207	NR_028409.1	n.234G>T		non_coding_transcript_exon_variant	Exon 3 of 5
LINC00207	NR_028410.1	n.167G>T		non_coding_transcript_exon_variant	Exon 2 of 4
LINC00207	NR_028411.1	n.167G>T		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00207	ENST00000603530.6	n.207G>T		non_coding_transcript_exon_variant	Exon 2 of 4	1
LINC00207	ENST00000605505.1	n.222G>T		non_coding_transcript_exon_variant	Exon 3 of 5	1
LINC00207	ENST00000334566.10	n.197G>T		non_coding_transcript_exon_variant	Exon 2 of 4	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 382152 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 217536

African (AFR) AF: 0.00 AC: 0 AN: 10514

American (AMR) AF: 0.00 AC: 0 AN: 36288

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11732

East Asian (EAS) AF: 0.00 AC: 0 AN: 13174

South Asian (SAS) AF: 0.00 AC: 0 AN: 66710

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32294

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2854

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 191880

Other (OTH) AF: 0.00 AC: 0 AN: 16706

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.66
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;