rs4949400
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178865.5(SERINC2):c.393-45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 1,414,230 control chromosomes in the GnomAD database, including 196,224 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.44 ( 16981 hom., cov: 33)
Exomes 𝑓: 0.52 ( 179243 hom. )
Consequence
SERINC2
NM_178865.5 intron
NM_178865.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0340
Genes affected
SERINC2 (HGNC:23231): (serine incorporator 2) Predicted to be involved in several processes, including phosphatidylserine metabolic process; positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity; and positive regulation of serine C-palmitoyltransferase activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERINC2 | NM_178865.5 | c.393-45T>C | intron_variant | ENST00000373709.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERINC2 | ENST00000373709.8 | c.393-45T>C | intron_variant | 1 | NM_178865.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.441 AC: 67060AN: 152046Hom.: 16980 Cov.: 33
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GnomAD3 exomes AF: 0.479 AC: 119645AN: 249988Hom.: 30840 AF XY: 0.483 AC XY: 65347AN XY: 135214
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GnomAD4 exome AF: 0.523 AC: 659960AN: 1262066Hom.: 179243 Cov.: 18 AF XY: 0.520 AC XY: 331943AN XY: 637942
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GnomAD4 genome ? AF: 0.441 AC: 67060AN: 152164Hom.: 16981 Cov.: 33 AF XY: 0.437 AC XY: 32526AN XY: 74384
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at