chr16-30899492-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001330.5(CTF1):c.103C>A(p.His35Asn) 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 1,612,296 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_001330.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTF1 | NM_001330.5 | c.103C>A | p.His35Asn | missense_variant | 2/3 | ENST00000279804.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTF1 | ENST00000279804.3 | c.103C>A | p.His35Asn | missense_variant | 2/3 | 1 | NM_001330.5 | P3 | |
CTF1 | ENST00000395019.3 | c.100C>A | p.His34Asn | missense_variant | 2/3 | 1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151572Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250646Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135544
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460724Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726684
GnomAD4 genome AF: 0.00000660 AC: 1AN: 151572Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74024
ClinVar
Submissions by phenotype
Dilated Cardiomyopathy, Dominant Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 10, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with CTF1-related conditions. This variant is present in population databases (rs771080334, gnomAD 0.006%). This sequence change replaces histidine, which is basic and polar, with asparagine, which is neutral and polar, at codon 35 of the CTF1 protein (p.His35Asn). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at