rs4957374
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000065.5(C6):c.2102-50T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 1,566,516 control chromosomes in the GnomAD database, including 567,101 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 0.86 ( 56982 hom., cov: 33)
Exomes 𝑓: 0.85 ( 510119 hom. )
Consequence
C6
NM_000065.5 intron
NM_000065.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.839
Genes affected
C6 (HGNC:1339): (complement C6) This gene encodes a component of the complement cascade. The encoded protein is part of the membrane attack complex that can be incorporated into the cell membrane and cause cell lysis. Mutations in this gene are associated with complement component-6 deficiency. Transcript variants encoding the same protein have been described.[provided by RefSeq, Nov 2012]
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C6 | NM_000065.5 | c.2102-50T>G | intron_variant | ENST00000337836.10 | |||
LOC105374739 | XR_001742650.2 | n.887-7265A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C6 | ENST00000337836.10 | c.2102-50T>G | intron_variant | 1 | NM_000065.5 | P1 | |||
C6 | ENST00000263413.7 | c.2102-50T>G | intron_variant | 1 | P1 | ||||
C6 | ENST00000461473.1 | n.134-50T>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.864 AC: 131461AN: 152092Hom.: 56922 Cov.: 33
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GnomAD3 exomes AF: 0.858 AC: 209592AN: 244180Hom.: 90149 AF XY: 0.855 AC XY: 112963AN XY: 132108
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GnomAD4 exome AF: 0.849 AC: 1200650AN: 1414306Hom.: 510119 Cov.: 23 AF XY: 0.849 AC XY: 599275AN XY: 706056
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GnomAD4 genome ? AF: 0.864 AC: 131579AN: 152210Hom.: 56982 Cov.: 33 AF XY: 0.864 AC XY: 64287AN XY: 74410
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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
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at