chr6-108868969-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032131.6(ARMC2):c.437C>T(p.Pro146Leu) 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 1,613,280 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032131.6 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 |
---|---|---|---|---|---|---|---|
ARMC2 | NM_032131.6 | c.437C>T | p.Pro146Leu | missense_variant | 4/18 | ENST00000392644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMC2 | ENST00000392644.9 | c.437C>T | p.Pro146Leu | missense_variant | 4/18 | 1 | NM_032131.6 | P1 | |
ARMC2 | ENST00000237512.4 | c.437C>T | p.Pro146Leu | missense_variant | 4/5 | 2 | |||
ARMC2 | ENST00000368972.7 | c.-59C>T | 5_prime_UTR_variant | 3/17 | 2 | ||||
ARMC2 | ENST00000414610.1 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000680 AC: 17AN: 249928Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135172
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1460996Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 726786
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 14, 2023 | The c.437C>T (p.P146L) alteration is located in exon 4 (coding exon 3) of the ARMC2 gene. This alteration results from a C to T substitution at nucleotide position 437, causing the proline (P) at amino acid position 146 to be replaced by a leucine (L). 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