1-54731487-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004623.5(TTC4):c.683C>T(p.Ala228Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,613,828 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004623.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTC4 | ENST00000371281.4 | c.683C>T | p.Ala228Val | missense_variant, splice_region_variant | Exon 7 of 10 | 1 | NM_004623.5 | ENSP00000360329.3 | ||
MROH7-TTC4 | ENST00000414150.6 | n.*385C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 30 of 33 | 2 | ENSP00000410192.2 | ||||
MROH7-TTC4 | ENST00000414150.6 | n.*385C>T | 3_prime_UTR_variant | Exon 30 of 33 | 2 | ENSP00000410192.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152174Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250534Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135374
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461536Hom.: 1 Cov.: 32 AF XY: 0.0000426 AC XY: 31AN XY: 727080
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152292Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.683C>T (p.A228V) alteration is located in exon 7 (coding exon 7) of the TTC4 gene. This alteration results from a C to T substitution at nucleotide position 683, causing the alanine (A) at amino acid position 228 to be replaced by a valine (V). 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