chr10-22998148-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_173081.5(ARMC3):c.1176C>T(p.Asn392=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000607 in 1,613,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_173081.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARMC3 | NM_173081.5 | c.1176C>T | p.Asn392= | splice_region_variant, synonymous_variant | 11/19 | ENST00000298032.10 | |
LOC107984215 | XR_001747394.2 | n.555-2330G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARMC3 | ENST00000298032.10 | c.1176C>T | p.Asn392= | splice_region_variant, synonymous_variant | 11/19 | 1 | NM_173081.5 | A1 | |
ENST00000655462.1 | n.117-31830G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000521 AC: 13AN: 249550Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134982
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461142Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 726830
GnomAD4 genome ? AF: 0.000276 AC: 42AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74488
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at