chr15-100402747-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001378789.1(CERS3):c.1118G>A(p.Arg373Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,614,162 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001378789.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CERS3 | NM_001378789.1 | c.1118G>A | p.Arg373Lys | missense_variant | 12/12 | ENST00000679737.1 | |
CERS3-AS1 | NR_120374.1 | n.211+2822C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERS3 | ENST00000679737.1 | c.1118G>A | p.Arg373Lys | missense_variant | 12/12 | NM_001378789.1 | P1 | ||
CERS3-AS1 | ENST00000560643.1 | n.51+2822C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00529 AC: 805AN: 152178Hom.: 9 Cov.: 33
GnomAD3 exomes AF: 0.00130 AC: 328AN: 251420Hom.: 2 AF XY: 0.000780 AC XY: 106AN XY: 135888
GnomAD4 exome AF: 0.000568 AC: 830AN: 1461866Hom.: 5 Cov.: 30 AF XY: 0.000441 AC XY: 321AN XY: 727236
GnomAD4 genome ? AF: 0.00531 AC: 808AN: 152296Hom.: 9 Cov.: 33 AF XY: 0.00509 AC XY: 379AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 12, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at