chr1-31424776-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_178865.5(SERINC2):c.295C>T(p.Arg99Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,612,246 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R99H) has been classified as Uncertain significance.
Frequency
Consequence
NM_178865.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERINC2 | NM_178865.5 | c.295C>T | p.Arg99Cys | missense_variant | 3/10 | ENST00000373709.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERINC2 | ENST00000373709.8 | c.295C>T | p.Arg99Cys | missense_variant | 3/10 | 1 | NM_178865.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000449 AC: 11AN: 244916Hom.: 0 AF XY: 0.0000676 AC XY: 9AN XY: 133044
GnomAD4 exome AF: 0.0000329 AC: 48AN: 1460040Hom.: 1 Cov.: 33 AF XY: 0.0000317 AC XY: 23AN XY: 726154
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 16, 2023 | The c.322C>T (p.R108C) alteration is located in exon 4 (coding exon 4) of the SERINC2 gene. This alteration results from a C to T substitution at nucleotide position 322, causing the arginine (R) at amino acid position 108 to be replaced by a cysteine (C). 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