rs2484992
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_134478.1(LINC02664):n.317+34970T>C 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 0.801 in 152,138 control chromosomes in the GnomAD database, including 54,364 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+34970T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02664 | ENST00000605929.1 | n.317+34970T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
ZEB1-AS1 | ENST00000605946.1 | n.178-16687A>G | intron_variant, non_coding_transcript_variant | 5 | |||||
LINC02664 | ENST00000662544.1 | n.389+16305T>C | intron_variant, non_coding_transcript_variant | ||||||
LINC02664 | ENST00000669722.1 | n.608+16305T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.802 AC: 121913AN: 152020Hom.: 54358 Cov.: 31
GnomAD4 genome ? AF: 0.801 AC: 121929AN: 152138Hom.: 54364 Cov.: 31 AF XY: 0.806 AC XY: 59938AN XY: 74398
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at