14-58138571-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001872.4(ARMH4):āc.788A>Gā(p.Asp263Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,614,214 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.788A>G | p.Asp263Gly | missense_variant | 2/8 | ENST00000267485.7 | NP_001001872.2 | |
ARMH4 | NM_001320173.3 | c.788A>G | p.Asp263Gly | missense_variant | 2/5 | NP_001307102.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARMH4 | ENST00000267485.7 | c.788A>G | p.Asp263Gly | missense_variant | 2/8 | 1 | NM_001001872.4 | ENSP00000267485 | P1 | |
ARMH4 | ENST00000334342.5 | n.953A>G | non_coding_transcript_exon_variant | 2/5 | 1 | |||||
ARMH4 | ENST00000557175.5 | n.671A>G | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251446Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135902
GnomAD4 exome AF: 0.000156 AC: 228AN: 1461892Hom.: 0 Cov.: 33 AF XY: 0.000142 AC XY: 103AN XY: 727246
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.788A>G (p.D263G) alteration is located in exon 2 (coding exon 1) of the C14orf37 gene. This alteration results from a A to G substitution at nucleotide position 788, causing the aspartic acid (D) at amino acid position 263 to be replaced by a glycine (G). 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