rs1250307
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_134478.1(LINC02664):n.317+18846G>A 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 0.803 in 152,202 control chromosomes in the GnomAD database, including 54,454 homozygotes. 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_134478.1 intron, non_coding_transcript
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC02664 | NR_134478.1 | n.317+18846G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02664 | ENST00000605929.1 | n.317+18846G>A | intron_variant, non_coding_transcript_variant | 2 | |||||
ZEB1-AS1 | ENST00000605946.1 | n.178-563C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
LINC02664 | ENST00000662544.1 | n.389+181G>A | intron_variant, non_coding_transcript_variant | ||||||
LINC02664 | ENST00000669722.1 | n.608+181G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.803 AC: 122173AN: 152084Hom.: 54451 Cov.: 33
GnomAD4 genome ? AF: 0.803 AC: 122187AN: 152202Hom.: 54454 Cov.: 33 AF XY: 0.807 AC XY: 60027AN XY: 74414
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at