chr17-42799198-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173478.3(CNTD1):c.131C>T(p.Ser44Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173478.3 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 |
---|---|---|---|---|---|---|---|---|
CNTD1 | NM_173478.3 | c.131C>T | p.Ser44Leu | missense_variant | 1/7 | ENST00000588408.6 | NP_775749.2 | |
CNTD1 | NM_001330222.2 | c.-81+180C>T | intron_variant | NP_001317151.1 | ||||
CNTD1 | XM_024450569.2 | c.13+368C>T | intron_variant | XP_024306337.1 | ||||
CNTD1 | XM_011524311.3 | c.-5+368C>T | intron_variant | XP_011522613.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTD1 | ENST00000588408.6 | c.131C>T | p.Ser44Leu | missense_variant | 1/7 | 1 | NM_173478.3 | ENSP00000465204.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152106Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000839 AC: 21AN: 250228Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135522
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461744Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727162
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152224Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.131C>T (p.S44L) alteration is located in exon 1 (coding exon 1) of the CNTD1 gene. This alteration results from a C to T substitution at nucleotide position 131, causing the serine (S) at amino acid position 44 to be replaced by a leucine (L). 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