chr1-31424845-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_178865.5(SERINC2):c.364C>T(p.Arg122Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00593 in 1,611,598 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R122G) has been classified as Likely benign.
Frequency
Consequence
NM_178865.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERINC2 | NM_178865.5 | c.364C>T | p.Arg122Trp | missense_variant | 3/10 | ENST00000373709.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERINC2 | ENST00000373709.8 | c.364C>T | p.Arg122Trp | missense_variant | 3/10 | 1 | NM_178865.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00429 AC: 653AN: 152106Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00402 AC: 959AN: 238622Hom.: 3 AF XY: 0.00408 AC XY: 535AN XY: 131058
GnomAD4 exome AF: 0.00610 AC: 8898AN: 1459374Hom.: 34 Cov.: 33 AF XY: 0.00609 AC XY: 4422AN XY: 725892
GnomAD4 genome AF: 0.00429 AC: 653AN: 152224Hom.: 4 Cov.: 32 AF XY: 0.00382 AC XY: 284AN XY: 74422
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 | SERINC2: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at