NM_031956.4:c.800-1G>A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_031956.4(TTC29):c.800-1G>A variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.000371 in 1,463,458 control chromosomes in the GnomAD database, including 1 homozygotes. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Consequence
NM_031956.4 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTC29 | NM_031956.4 | c.800-1G>A | splice_acceptor_variant, intron_variant | Intron 7 of 12 | ENST00000325106.9 | NP_114162.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTC29 | ENST00000325106.9 | c.800-1G>A | splice_acceptor_variant, intron_variant | Intron 7 of 12 | 1 | NM_031956.4 | ENSP00000316740.4 | |||
TTC29 | ENST00000508306.5 | n.800-1G>A | splice_acceptor_variant, intron_variant | Intron 7 of 13 | 1 | ENSP00000422648.1 | ||||
TTC29 | ENST00000513335.5 | c.878-1G>A | splice_acceptor_variant, intron_variant | Intron 8 of 13 | 2 | ENSP00000423505.1 | ||||
TTC29 | ENST00000504425.5 | c.800-1G>A | splice_acceptor_variant, intron_variant | Intron 7 of 12 | 5 | ENSP00000425778.1 |
Frequencies
GnomAD3 genomes AF: 0.000257 AC: 39AN: 152006Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000173 AC: 25AN: 144322Hom.: 0 AF XY: 0.000143 AC XY: 11AN XY: 77150
GnomAD4 exome AF: 0.000384 AC: 504AN: 1311334Hom.: 1 Cov.: 21 AF XY: 0.000352 AC XY: 229AN XY: 650012
GnomAD4 genome AF: 0.000256 AC: 39AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74372
ClinVar
Submissions by phenotype
TTC29-related condition Pathogenic:1
The TTC29 c.878-1G>A variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.043% of alleles in individuals of Latino descent in gnomAD. Variants that disrupt the consensus splice acceptor site in TTC29 are expected to be pathogenic. This variant is interpreted as likely pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at