chr4-158671796-G-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001008393.4(C4orf46):c.6C>A(p.Ala2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00342 in 1,538,622 control chromosomes in the GnomAD database, including 144 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.018 ( 82 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 62 hom. )
Consequence
C4orf46
NM_001008393.4 synonymous
NM_001008393.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.06
Genes affected
C4orf46 (HGNC:27320): (chromosome 4 open reading frame 46) This gene encodes a small, conserved protein of unknown function that is expressed in a variety of tissues. There are pseudogenes for this gene on chromosomes 6, 8, 16, and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 4-158671796-G-T is Benign according to our data. Variant chr4-158671796-G-T is described in ClinVar as [Benign]. Clinvar id is 1283566.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-2.07 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0589 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C4orf46 | NM_001008393.4 | c.6C>A | p.Ala2= | synonymous_variant | 1/2 | ENST00000379205.5 | |
C4orf46 | NR_077234.2 | n.60+201C>A | intron_variant, non_coding_transcript_variant | ||||
C4orf46 | NR_077235.2 | n.60+201C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C4orf46 | ENST00000379205.5 | c.6C>A | p.Ala2= | synonymous_variant | 1/2 | 1 | NM_001008393.4 | P1 | |
C4orf46 | ENST00000508836.1 | n.259+201C>A | intron_variant, non_coding_transcript_variant | 1 | |||||
C4orf46 | ENST00000508457.1 | c.6C>A | p.Ala2= | synonymous_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0178 AC: 2707AN: 152120Hom.: 81 Cov.: 32
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GnomAD3 exomes AF: 0.00439 AC: 619AN: 141056Hom.: 18 AF XY: 0.00306 AC XY: 228AN XY: 74440
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GnomAD4 exome AF: 0.00184 AC: 2550AN: 1386384Hom.: 62 Cov.: 31 AF XY: 0.00165 AC XY: 1130AN XY: 683286
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GnomAD4 genome AF: 0.0178 AC: 2713AN: 152238Hom.: 82 Cov.: 32 AF XY: 0.0173 AC XY: 1291AN XY: 74454
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | - - |
Computational 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