5-80151081-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001174072.3(SERINC5):c.987-133C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 698,702 control chromosomes in the GnomAD database, including 13,360 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 0.19 ( 2847 hom., cov: 33)
Exomes 𝑓: 0.19 ( 10513 hom. )
Consequence
SERINC5
NM_001174072.3 intron
NM_001174072.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.240
Genes affected
SERINC5 (HGNC:18825): (serine incorporator 5) Predicted to enable L-serine transmembrane transporter activity. Involved in defense response to virus; detection of virus; and innate immune response. Located in several cellular components, including centrosome; cytosol; and plasma membrane. [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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERINC5 | NM_001174072.3 | c.987-133C>T | intron_variant | ENST00000507668.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERINC5 | ENST00000507668.7 | c.987-133C>T | intron_variant | 2 | NM_001174072.3 | P1 | |||
SERINC5 | ENST00000509193.5 | c.987-133C>T | intron_variant | 1 | |||||
SERINC5 | ENST00000512972.6 | c.987-133C>T | intron_variant, NMD_transcript_variant | 2 | |||||
SERINC5 | ENST00000632581.1 | c.981-133C>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.191 AC: 29056AN: 152024Hom.: 2843 Cov.: 33
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GnomAD4 exome AF: 0.189 AC: 103106AN: 546560Hom.: 10513 AF XY: 0.194 AC XY: 56991AN XY: 294126
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GnomAD4 genome AF: 0.191 AC: 29086AN: 152142Hom.: 2847 Cov.: 33 AF XY: 0.189 AC XY: 14085AN XY: 74370
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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