chr4-99653155-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001354435.2(C4orf54):c.1494G>A(p.Pro498Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00284 in 1,536,180 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0028 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 21 hom. )
Consequence
C4orf54
NM_001354435.2 synonymous
NM_001354435.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.04
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant 4-99653155-C-T is Benign according to our data. Variant chr4-99653155-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2654975.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.04 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 6 gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00283 AC: 430AN: 152184Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00430 AC: 580AN: 134920Hom.: 7 AF XY: 0.00468 AC XY: 344AN XY: 73434
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GnomAD4 exome AF: 0.00284 AC: 3933AN: 1383878Hom.: 21 Cov.: 38 AF XY: 0.00307 AC XY: 2098AN XY: 682880
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GnomAD4 genome AF: 0.00280 AC: 427AN: 152302Hom.: 6 Cov.: 32 AF XY: 0.00289 AC XY: 215AN XY: 74468
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
C4orf54: BP4, BP7 -
Computational 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