chr1-2569899-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_121638.1(LOC100996583):n.71+3294C>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 0.516 in 151,820 control chromosomes in the GnomAD database, including 20,478 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_121638.1 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 |
---|---|---|---|---|---|---|---|
LOC100996583 | NR_121638.1 | n.71+3294C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000456687.3 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.516 AC: 78327AN: 151662Hom.: 20464 Cov.: 31
GnomAD4 exome AF: 0.325 AC: 13AN: 40Hom.: 3 Cov.: 0 AF XY: 0.333 AC XY: 8AN XY: 24
GnomAD4 genome AF: 0.516 AC: 78370AN: 151780Hom.: 20475 Cov.: 31 AF XY: 0.520 AC XY: 38559AN XY: 74184
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at