chr14-58133258-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001872.4(ARMH4):c.1453C>A(p.Leu485Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001872.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARMH4 | NM_001001872.4 | c.1453C>A | p.Leu485Ile | missense_variant | 3/8 | ENST00000267485.7 | NP_001001872.2 | |
ARMH4 | NM_001320173.3 | c.1453C>A | p.Leu485Ile | missense_variant | 3/5 | NP_001307102.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARMH4 | ENST00000267485.7 | c.1453C>A | p.Leu485Ile | missense_variant | 3/8 | 1 | NM_001001872.4 | ENSP00000267485 | P1 | |
ARMH4 | ENST00000334342.5 | n.1618C>A | non_coding_transcript_exon_variant | 3/5 | 1 | |||||
ARMH4 | ENST00000557175.5 | n.978C>A | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152088Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251482Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135912
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727244
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152206Hom.: 0 Cov.: 30 AF XY: 0.0000806 AC XY: 6AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 18, 2021 | The c.1453C>A (p.L485I) alteration is located in exon 3 (coding exon 2) of the C14orf37 gene. This alteration results from a C to A substitution at nucleotide position 1453, causing the leucine (L) at amino acid position 485 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at