chr2-103958986-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000688553.1(LINC01965):n.210+84541A>G 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 0.911 in 152,190 control chromosomes in the GnomAD database, including 63,319 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
ENST00000688553.1 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 |
---|---|---|---|---|---|---|---|
LINC01965 | XR_001739621.2 | n.157+84541A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01965 | ENST00000688553.1 | n.210+84541A>G | intron_variant, non_coding_transcript_variant | ||||||
LINC01965 | ENST00000537492.5 | n.136+84541A>G | intron_variant, non_coding_transcript_variant | 4 | |||||
LINC01965 | ENST00000544869.5 | n.115+84541A>G | intron_variant, non_coding_transcript_variant | 4 | |||||
LINC01965 | ENST00000655320.1 | n.116-308A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.911 AC: 138544AN: 152072Hom.: 63255 Cov.: 31
GnomAD4 genome ? AF: 0.911 AC: 138667AN: 152190Hom.: 63319 Cov.: 31 AF XY: 0.915 AC XY: 68068AN XY: 74414
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at