1-52033308-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138417.3(KTI12):c.454C>T(p.Leu152Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138417.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KTI12 | NM_138417.3 | c.454C>T | p.Leu152Phe | missense_variant | 1/1 | ENST00000371614.2 | NP_612426.1 | |
TXNDC12 | NM_015913.4 | c.159-4678C>T | intron_variant | ENST00000371626.9 | NP_056997.1 | |||
TXNDC12 | NR_046405.1 | n.1977C>T | non_coding_transcript_exon_variant | 3/3 | ||||
TXNDC12 | NR_046406.1 | n.1854C>T | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KTI12 | ENST00000371614.2 | c.454C>T | p.Leu152Phe | missense_variant | 1/1 | NM_138417.3 | ENSP00000360676 | P1 | ||
TXNDC12 | ENST00000371626.9 | c.159-4678C>T | intron_variant | 1 | NM_015913.4 | ENSP00000360688 | P1 | |||
TXNDC12 | ENST00000610127.2 | c.*734C>T | 3_prime_UTR_variant | 3/3 | 2 | ENSP00000476401 | ||||
TXNDC12 | ENST00000472624.5 | c.159-2760C>T | intron_variant, NMD_transcript_variant | 5 | ENSP00000477120 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250672Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135610
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461620Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727102
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2024 | The c.454C>T (p.L152F) alteration is located in exon 1 (coding exon 1) of the KTI12 gene. This alteration results from a C to T substitution at nucleotide position 454, causing the leucine (L) at amino acid position 152 to be replaced by a phenylalanine (F). 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