chr1-150966161-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_022075.5(CERS2):āc.1130G>Cā(p.Arg377Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000689 in 1,610,470 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_022075.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CERS2 | NM_022075.5 | c.1130G>C | p.Arg377Pro | missense_variant | 11/11 | ENST00000368954.10 | |
CERS2 | NM_181746.4 | c.1130G>C | p.Arg377Pro | missense_variant | 11/11 | ||
CERS2 | XM_011509451.3 | c.1190G>C | p.Arg397Pro | missense_variant | 11/11 | ||
CERS2 | XM_011509452.4 | c.1130G>C | p.Arg377Pro | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERS2 | ENST00000368954.10 | c.1130G>C | p.Arg377Pro | missense_variant | 11/11 | 1 | NM_022075.5 | P1 | |
ENST00000561111.2 | n.547C>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152120Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000485 AC: 12AN: 247472Hom.: 0 AF XY: 0.0000448 AC XY: 6AN XY: 133984
GnomAD4 exome AF: 0.0000686 AC: 100AN: 1458350Hom.: 0 Cov.: 35 AF XY: 0.0000593 AC XY: 43AN XY: 725648
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152120Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2023 | The c.1130G>C (p.R377P) alteration is located in exon 11 (coding exon 10) of the CERS2 gene. This alteration results from a G to C substitution at nucleotide position 1130, causing the arginine (R) at amino acid position 377 to be replaced by a proline (P). 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