chr1-150966805-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022075.5(CERS2):c.799G>A(p.Val267Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00557 in 1,614,048 control chromosomes in the GnomAD database, including 32 homozygotes. 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_022075.5 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 |
---|---|---|---|---|---|---|---|
CERS2 | NM_022075.5 | c.799G>A | p.Val267Ile | missense_variant | 9/11 | ENST00000368954.10 | |
CERS2 | NM_181746.4 | c.799G>A | p.Val267Ile | missense_variant | 9/11 | ||
CERS2 | XM_011509451.3 | c.859G>A | p.Val287Ile | missense_variant | 9/11 | ||
CERS2 | XM_011509452.4 | c.799G>A | p.Val267Ile | missense_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERS2 | ENST00000368954.10 | c.799G>A | p.Val267Ile | missense_variant | 9/11 | 1 | NM_022075.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00406 AC: 617AN: 152112Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00435 AC: 1093AN: 251478Hom.: 2 AF XY: 0.00419 AC XY: 569AN XY: 135912
GnomAD4 exome AF: 0.00573 AC: 8369AN: 1461818Hom.: 30 Cov.: 33 AF XY: 0.00559 AC XY: 4067AN XY: 727222
GnomAD4 genome ? AF: 0.00405 AC: 617AN: 152230Hom.: 2 Cov.: 32 AF XY: 0.00417 AC XY: 310AN XY: 74426
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | CERS2: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at