rs281865168
Variant summary
Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PVS1PM2PP3_StrongPP5
The NM_003322.6(TULP1):c.1495+1G>C variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in Lovd as Likely pathogenic (no stars).
Frequency
Consequence
NM_003322.6 splice_donor
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TULP1 | NM_003322.6 | c.1495+1G>C | splice_donor_variant | ENST00000229771.11 | |||
LOC124901309 | XR_007059561.1 | n.75+1773C>G | intron_variant, non_coding_transcript_variant | ||||
TULP1 | NM_001289395.2 | c.1336+1G>C | splice_donor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TULP1 | ENST00000229771.11 | c.1495+1G>C | splice_donor_variant | 1 | NM_003322.6 | P4 | |||
TULP1 | ENST00000322263.8 | c.1336+1G>C | splice_donor_variant | 1 | A2 | ||||
TULP1 | ENST00000614066.4 | c.1489+1G>C | splice_donor_variant | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461696Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727154
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at