rs36059701
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002448.3(MSX1):āc.119C>Gā(p.Ala40Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,500,962 control chromosomes in the GnomAD database, including 18,800 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_002448.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSX1 | NM_002448.3 | c.119C>G | p.Ala40Gly | missense_variant | 1/2 | ENST00000382723.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSX1 | ENST00000382723.5 | c.119C>G | p.Ala40Gly | missense_variant | 1/2 | 1 | NM_002448.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.140 AC: 21331AN: 151922Hom.: 1595 Cov.: 33
GnomAD3 exomes AF: 0.150 AC: 15047AN: 100178Hom.: 1241 AF XY: 0.149 AC XY: 8314AN XY: 55658
GnomAD4 exome AF: 0.156 AC: 210803AN: 1348932Hom.: 17206 Cov.: 34 AF XY: 0.155 AC XY: 103375AN XY: 665042
GnomAD4 genome ? AF: 0.140 AC: 21327AN: 152030Hom.: 1594 Cov.: 33 AF XY: 0.141 AC XY: 10501AN XY: 74318
ClinVar
Submissions by phenotype
Hypoplastic enamel-onycholysis-hypohidrosis syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | This variant is associated with the following publications: (PMID: 28965043, 28204848, 16723652, 15379328, 21866112, 25565750, 21740177) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at