chr2-32666721-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017735.5(TTC27):c.892A>C(p.Asn298His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000124 in 1,613,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017735.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC27 | NM_017735.5 | c.892A>C | p.Asn298His | missense_variant | 7/20 | ENST00000317907.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC27 | ENST00000317907.9 | c.892A>C | p.Asn298His | missense_variant | 7/20 | 1 | NM_017735.5 | P1 | |
TTC27 | ENST00000647819.1 | c.892A>C | p.Asn298His | missense_variant, NMD_transcript_variant | 7/22 | ||||
TTC27 | ENST00000454690.1 | c.89-12135A>C | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000115 AC: 29AN: 251270Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135780
GnomAD4 exome AF: 0.000129 AC: 188AN: 1461788Hom.: 0 Cov.: 30 AF XY: 0.000133 AC XY: 97AN XY: 727186
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.892A>C (p.N298H) alteration is located in exon 7 (coding exon 7) of the TTC27 gene. This alteration results from a A to C substitution at nucleotide position 892, causing the asparagine (N) at amino acid position 298 to be replaced by a histidine (H). 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