chr6-35748863-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001286574.2(ARMC12):c.1016C>T(p.Thr339Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000224 in 1,608,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001286574.2 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 | UniProt |
---|---|---|---|---|---|---|---|
ARMC12 | NM_001286574.2 | c.1016C>T | p.Thr339Met | missense_variant | 6/6 | ENST00000373866.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMC12 | ENST00000373866.4 | c.1016C>T | p.Thr339Met | missense_variant | 6/6 | 3 | NM_001286574.2 | A1 | |
ARMC12 | ENST00000288065.6 | c.1097C>T | p.Thr366Met | missense_variant | 6/6 | 1 | P3 | ||
ARMC12 | ENST00000373869.7 | c.986C>T | p.Thr329Met | missense_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000409 AC: 10AN: 244278Hom.: 0 AF XY: 0.0000302 AC XY: 4AN XY: 132624
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1456132Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 724294
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2021 | The c.1097C>T (p.T366M) alteration is located in exon 6 (coding exon 6) of the ARMC12 gene. This alteration results from a C to T substitution at nucleotide position 1097, causing the threonine (T) at amino acid position 366 to be replaced by a methionine (M). 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