NM_001267727.2:c.1478T>C
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001267727.2(ARSG):c.1478T>C(p.Ile493Thr) variant causes a missense change. The variant allele was found at a frequency of 0.003 in 1,614,120 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001267727.2 missense
Scores
Clinical Significance
Conservation
Publications
- Acrodysostosis 1 with or without hormone resistanceInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
- acrodysostosis with multiple hormone resistanceInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Illumina, Orphanet
- Carney complex, type 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- pigmented nodular adrenocortical disease, primary, 1Inheritance: AD Classification: STRONG, MODERATE Submitted by: Genomics England PanelApp, Ambry Genetics
- acrodysostosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Carney complexInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- familial atrial myxomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- primary pigmented nodular adrenocortical diseaseInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARSG | NM_001267727.2 | c.1478T>C | p.Ile493Thr | missense_variant | Exon 12 of 12 | ENST00000621439.5 | NP_001254656.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00235 AC: 357AN: 152112Hom.: 1 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00255 AC: 640AN: 251436 AF XY: 0.00271 show subpopulations
GnomAD4 exome AF: 0.00307 AC: 4488AN: 1461890Hom.: 10 Cov.: 31 AF XY: 0.00300 AC XY: 2184AN XY: 727244 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00235 AC: 357AN: 152230Hom.: 1 Cov.: 32 AF XY: 0.00212 AC XY: 158AN XY: 74426 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:3
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ARSG: BP4 -
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ARSG-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at