rs7642243
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The XR_001740544.2(LOC105374304):n.1131-1G>T variant causes a splice acceptor, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 151,824 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
XR_001740544.2 splice_acceptor, non_coding_transcript
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105374304 | XR_001740544.2 | n.1131-1G>T | splice_acceptor_variant, non_coding_transcript_variant | ||||
LOC124909479 | XR_007096240.1 | n.560-78C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCYT1A | ENST00000441879.5 | c.515G>T | p.Arg172Met | missense_variant | 6/6 | 3 | |||
SLC51A | ENST00000416660.1 | c.-47-78C>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151824Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 0
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151824Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74130
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at