rs241039
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001256299.3(LINC02210-CRHR1):c.-493+7149A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 152,174 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
Consequence
NM_001256299.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC02210-CRHR1 | NM_001256299.3 | c.-493+7149A>G | intron_variant | ||||
LINC02210 | NR_138260.1 | n.624+6701A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02210 | ENST00000455565.5 | n.1957A>G | non_coding_transcript_exon_variant | 4/4 | 1 | ||||
LINC02210 | ENST00000591271.5 | n.422+7149A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
LINC02210 | ENST00000586362.1 | n.107A>G | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152174Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 8Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 4
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at