chr2-171554632-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000375252.3(CYBRD1):c.457G>A(p.Ala153Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000375252.3 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 | UniProt |
---|---|---|---|---|---|---|---|
CYBRD1 | NM_024843.4 | c.666G>A | p.Pro222= | synonymous_variant | 4/4 | ENST00000321348.9 | |
CYBRD1 | NM_001127383.2 | c.457G>A | p.Ala153Thr | missense_variant | 3/3 | ||
CYBRD1 | NM_001256909.2 | c.492G>A | p.Pro164= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYBRD1 | ENST00000375252.3 | c.457G>A | p.Ala153Thr | missense_variant | 3/3 | 1 | |||
CYBRD1 | ENST00000321348.9 | c.666G>A | p.Pro222= | synonymous_variant | 4/4 | 1 | NM_024843.4 | P1 | |
CYBRD1 | ENST00000409484.5 | c.492G>A | p.Pro164= | synonymous_variant | 4/4 | 2 | |||
CYBRD1 | ENST00000445146.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250910Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135594
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1461720Hom.: 0 Cov.: 30 AF XY: 0.0000344 AC XY: 25AN XY: 727164
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74322
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 28, 2023 | 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