ENST00000603530.6:n.*206G>A – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000603530.6(LINC00207):n.207G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000262 in 382,152 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000026 ( 0 hom. )

Consequence

LINC00207
ENST00000603530.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00500

Publications

0 publications found

Variant links:

COSMIC-nc: COSV58000354

Genes affected

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

LINC00207 links:

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ACMG classification

Classification was made for transcript

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=0.033).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00207	NR_028409.1 link	n.234G>A	non_coding_transcript_exon_variant	Exon 3 of 5
LINC00207	NR_028410.1 link	n.167G>A	non_coding_transcript_exon_variant	Exon 2 of 4
LINC00207	NR_028411.1 link	n.167G>A	non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00207	ENST00000603530.6 link	n.207G>A	non_coding_transcript_exon_variant	Exon 2 of 4	1
LINC00207	ENST00000605505.1 link	n.222G>A	non_coding_transcript_exon_variant	Exon 3 of 5	1
LINC00207	ENST00000334566.10 link	n.197G>A	non_coding_transcript_exon_variant	Exon 2 of 4	5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000262

AC:

AN:

382152

Hom.:

Cov.:

AF XY:

0.00000460

AC XY:

AN XY:

217536

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10514

American (AMR)

AF:

0.00

AC:

AN:

36288

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11732

East Asian (EAS)

AF:

0.00

AC:

AN:

13174

South Asian (SAS)

AF:

0.0000150

AC:

AN:

66710

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32294

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2854

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

191880

Other (OTH)

AF:

0.00

AC:

AN:

16706

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.88

(source)

DANN

Benign

0.63

PhyloP100

0.0050

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over