rs143184428
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_020458.4(TTC7A):c.2015C>T(p.Ser672Phe) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000154 in 1,613,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S672P) has been classified as Likely benign.
Frequency
Consequence
NM_020458.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC7A | NM_020458.4 | c.2015C>T | p.Ser672Phe | missense_variant, splice_region_variant | 17/20 | ENST00000319190.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC7A | ENST00000319190.11 | c.2015C>T | p.Ser672Phe | missense_variant, splice_region_variant | 17/20 | 2 | NM_020458.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000279 AC: 70AN: 251098Hom.: 0 AF XY: 0.000250 AC XY: 34AN XY: 135748
GnomAD4 exome AF: 0.000158 AC: 231AN: 1461000Hom.: 0 Cov.: 31 AF XY: 0.000162 AC XY: 118AN XY: 726892
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74364
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.2015C>T (p.S672F) alteration is located in exon 17 (coding exon 17) of the TTC7A gene. This alteration results from a C to T substitution at nucleotide position 2015, causing the serine (S) at amino acid position 672 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Multiple gastrointestinal atresias Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at