14-58139302-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001001872.4(ARMH4):c.57C>T(p.Phe19=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,614,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
ARMH4
NM_001001872.4 synonymous
NM_001001872.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.160
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 14-58139302-G-A is Benign according to our data. Variant chr14-58139302-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2644258.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.16 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARMH4 | NM_001001872.4 | c.57C>T | p.Phe19= | synonymous_variant | 2/8 | ENST00000267485.7 | NP_001001872.2 | |
ARMH4 | NM_001320173.3 | c.57C>T | p.Phe19= | synonymous_variant | 2/5 | NP_001307102.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARMH4 | ENST00000267485.7 | c.57C>T | p.Phe19= | synonymous_variant | 2/8 | 1 | NM_001001872.4 | ENSP00000267485 | P1 | |
ARMH4 | ENST00000334342.5 | n.222C>T | non_coding_transcript_exon_variant | 2/5 | 1 | |||||
ARMH4 | ENST00000554218.1 | n.371C>T | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152156Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251446Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135894
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GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461884Hom.: 0 Cov.: 34 AF XY: 0.0000261 AC XY: 19AN XY: 727242
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GnomAD4 genome AF: 0.0000591 AC: 9AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74330
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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
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | ARMH4: BP4, BP7 - |
Computational scores
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Benign
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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