chr6-35748841-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001286574.2(ARMC12):c.994A>G(p.Ser332Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,612,342 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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.994A>G | p.Ser332Gly | missense_variant | 6/6 | ENST00000373866.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMC12 | ENST00000373866.4 | c.994A>G | p.Ser332Gly | missense_variant | 6/6 | 3 | NM_001286574.2 | A1 | |
ARMC12 | ENST00000288065.6 | c.1075A>G | p.Ser359Gly | missense_variant | 6/6 | 1 | P3 | ||
ARMC12 | ENST00000373869.7 | c.964A>G | p.Ser322Gly | missense_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000124 AC: 31AN: 249090Hom.: 0 AF XY: 0.0000965 AC XY: 13AN XY: 134698
GnomAD4 exome AF: 0.000111 AC: 162AN: 1459990Hom.: 1 Cov.: 30 AF XY: 0.0000909 AC XY: 66AN XY: 726258
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152352Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.1075A>G (p.S359G) alteration is located in exon 6 (coding exon 6) of the ARMC12 gene. This alteration results from a A to G substitution at nucleotide position 1075, causing the serine (S) at amino acid position 359 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