chr2-32630523-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_017735.5(TTC27):āc.89A>Gā(p.Glu30Gly) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000676 in 1,597,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 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 (ā ).
Frequency
Consequence
NM_017735.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC27 | NM_017735.5 | c.89A>G | p.Glu30Gly | missense_variant, splice_region_variant | 2/20 | ENST00000317907.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC27 | ENST00000317907.9 | c.89A>G | p.Glu30Gly | missense_variant, splice_region_variant | 2/20 | 1 | NM_017735.5 | P1 | |
TTC27 | ENST00000448773.5 | c.-62A>G | splice_region_variant, 5_prime_UTR_variant | 2/4 | 4 | ||||
TTC27 | ENST00000647819.1 | c.89A>G | p.Glu30Gly | missense_variant, splice_region_variant, NMD_transcript_variant | 2/22 | ||||
TTC27 | ENST00000454690.1 | c.88+2143A>G | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000417 AC: 10AN: 240010Hom.: 0 AF XY: 0.0000383 AC XY: 5AN XY: 130548
GnomAD4 exome AF: 0.0000706 AC: 102AN: 1445414Hom.: 0 Cov.: 28 AF XY: 0.0000751 AC XY: 54AN XY: 719152
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2024 | The c.89A>G (p.E30G) alteration is located in exon 2 (coding exon 2) of the TTC27 gene. This alteration results from a A to G substitution at nucleotide position 89, causing the glutamic acid (E) at amino acid position 30 to be replaced by a glycine (G). 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