14-58133255-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001001872.4(ARMH4):c.1456G>A(p.Glu486Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARMH4 | NM_001001872.4 | c.1456G>A | p.Glu486Lys | missense_variant | 3/8 | ENST00000267485.7 | NP_001001872.2 | |
ARMH4 | NM_001320173.3 | c.1456G>A | p.Glu486Lys | missense_variant | 3/5 | NP_001307102.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARMH4 | ENST00000267485.7 | c.1456G>A | p.Glu486Lys | missense_variant | 3/8 | 1 | NM_001001872.4 | ENSP00000267485 | P1 | |
ARMH4 | ENST00000334342.5 | n.1621G>A | non_coding_transcript_exon_variant | 3/5 | 1 | |||||
ARMH4 | ENST00000557175.5 | n.981G>A | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152000Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251488Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135916
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000316 AC XY: 23AN XY: 727244
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152000Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.1456G>A (p.E486K) alteration is located in exon 3 (coding exon 2) of the C14orf37 gene. This alteration results from a G to A substitution at nucleotide position 1456, causing the glutamic acid (E) at amino acid position 486 to be replaced by a lysine (K). 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