11-120228962-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_178507.4(OAF):c.642C>T(p.Cys214=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,612,604 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0057 ( 10 hom., cov: 34)
Exomes 𝑓: 0.00058 ( 4 hom. )
Consequence
OAF
NM_178507.4 synonymous
NM_178507.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.06
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 11-120228962-C-T is Benign according to our data. Variant chr11-120228962-C-T is described in ClinVar as [Benign]. Clinvar id is 735074.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.06 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00573 (873/152260) while in subpopulation AFR AF= 0.0192 (799/41546). AF 95% confidence interval is 0.0181. There are 10 homozygotes in gnomad4. There are 403 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAF | NM_178507.4 | c.642C>T | p.Cys214= | synonymous_variant | 4/4 | ENST00000328965.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAF | ENST00000328965.9 | c.642C>T | p.Cys214= | synonymous_variant | 4/4 | 1 | NM_178507.4 | P1 | |
OAF | ENST00000531220.1 | c.294C>T | p.Cys98= | synonymous_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00572 AC: 870AN: 152142Hom.: 10 Cov.: 34
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GnomAD3 exomes AF: 0.00139 AC: 345AN: 248312Hom.: 3 AF XY: 0.00109 AC XY: 147AN XY: 134996
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GnomAD4 exome AF: 0.000577 AC: 842AN: 1460344Hom.: 4 Cov.: 50 AF XY: 0.000484 AC XY: 352AN XY: 726542
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GnomAD4 genome AF: 0.00573 AC: 873AN: 152260Hom.: 10 Cov.: 34 AF XY: 0.00541 AC XY: 403AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 27, 2018 | - - |
Computational scores
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BayesDel_noAF
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at