Genetic Variant ENST00000603530.6:n.207G>A (chr22-44570564-G-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:

Genome browser will be placed here

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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