chr3-55279372-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NR_183740.1(LINC02030):n.484-6946A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000092 in 152,136 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
NR_183740.1 intron, non_coding_transcript
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 |
---|---|---|---|---|---|---|---|
LINC02030 | NR_183740.1 | n.484-6946A>T | intron_variant, non_coding_transcript_variant | ||||
LOC124906243 | XR_007095917.1 | n.100-12452T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02030 | ENST00000654581.1 | n.363-6946A>T | intron_variant, non_coding_transcript_variant | ||||||
LINC02030 | ENST00000662390.1 | n.321-6946A>T | intron_variant, non_coding_transcript_variant | ||||||
LINC02030 | ENST00000670191.1 | n.213-6946A>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152136Hom.: 0 Cov.: 34
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152136Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74298
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at