chr22-37311478-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_013385.5(CYTH4):c.908T>C(p.Ile303Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013385.5 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYTH4 | NM_013385.5 | c.908T>C | p.Ile303Thr | missense_variant | Exon 11 of 13 | ENST00000248901.11 | NP_037517.1 | |
CYTH4 | NM_001318024.2 | c.737T>C | p.Ile246Thr | missense_variant | Exon 11 of 13 | NP_001304953.1 | ||
LOC105373024 | XR_938231.2 | n.448A>G | non_coding_transcript_exon_variant | Exon 3 of 3 | ||||
LOC105373024 | XR_938232.3 | n.569A>G | non_coding_transcript_exon_variant | Exon 4 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYTH4 | ENST00000248901.11 | c.908T>C | p.Ile303Thr | missense_variant | Exon 11 of 13 | 1 | NM_013385.5 | ENSP00000248901.6 | ||
CYTH4 | ENST00000446506.1 | c.164T>C | p.Ile55Thr | missense_variant | Exon 3 of 5 | 4 | ENSP00000409579.1 | |||
CYTH4 | ENST00000462927.5 | n.1068T>C | non_coding_transcript_exon_variant | Exon 12 of 13 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251420Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135884
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461826Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727216
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.908T>C (p.I303T) alteration is located in exon 11 (coding exon 11) of the CYTH4 gene. This alteration results from a T to C substitution at nucleotide position 908, causing the isoleucine (I) at amino acid position 303 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at