2-171522589-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_024843.4(CYBRD1):c.44C>T(p.Ser15Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00153 in 1,611,586 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024843.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYBRD1 | NM_024843.4 | c.44C>T | p.Ser15Leu | missense_variant | 1/4 | ENST00000321348.9 | |
CYBRD1 | NM_001127383.2 | c.44C>T | p.Ser15Leu | missense_variant | 1/3 | ||
CYBRD1 | NM_001256909.2 | c.19+298C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYBRD1 | ENST00000321348.9 | c.44C>T | p.Ser15Leu | missense_variant | 1/4 | 1 | NM_024843.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000953 AC: 145AN: 152170Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00119 AC: 291AN: 243898Hom.: 2 AF XY: 0.00124 AC XY: 163AN XY: 131656
GnomAD4 exome AF: 0.00159 AC: 2318AN: 1459300Hom.: 3 Cov.: 33 AF XY: 0.00157 AC XY: 1137AN XY: 725616
GnomAD4 genome ? AF: 0.000952 AC: 145AN: 152286Hom.: 1 Cov.: 32 AF XY: 0.000766 AC XY: 57AN XY: 74452
ClinVar
Submissions by phenotype
CYBRD1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 03, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at