1-52033265-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_138417.3(KTI12):c.497C>T(p.Ala166Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,646 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 Likely benign (★).
Frequency
Consequence
NM_138417.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KTI12 | NM_138417.3 | c.497C>T | p.Ala166Val | missense_variant | 1/1 | ENST00000371614.2 | NP_612426.1 | |
TXNDC12 | NM_015913.4 | c.159-4635C>T | intron_variant | ENST00000371626.9 | NP_056997.1 | |||
TXNDC12 | NR_046405.1 | n.2020C>T | non_coding_transcript_exon_variant | 3/3 | ||||
TXNDC12 | NR_046406.1 | n.1897C>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.497C>T | p.Ala166Val | missense_variant | 1/1 | 6 | NM_138417.3 | ENSP00000360676.1 | ||
TXNDC12 | ENST00000371626.9 | c.159-4635C>T | intron_variant | 1 | NM_015913.4 | ENSP00000360688.4 | ||||
ENSG00000285839 | ENST00000648686.1 | n.86C>T | non_coding_transcript_exon_variant | 1/7 | ENSP00000498140.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461646Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727110
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.