rs771408025
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_002448.3(MSX1):c.95C>T(p.Ala32Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000851 in 1,491,764 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A32S) has been classified as Uncertain significance.
Frequency
Consequence
NM_002448.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSX1 | NM_002448.3 | c.95C>T | p.Ala32Val | missense_variant | 1/2 | ENST00000382723.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSX1 | ENST00000382723.5 | c.95C>T | p.Ala32Val | missense_variant | 1/2 | 1 | NM_002448.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000388 AC: 59AN: 152020Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000641 AC: 6AN: 93572Hom.: 0 AF XY: 0.0000964 AC XY: 5AN XY: 51886
GnomAD4 exome AF: 0.0000508 AC: 68AN: 1339636Hom.: 0 Cov.: 30 AF XY: 0.0000545 AC XY: 36AN XY: 660048
GnomAD4 genome ? AF: 0.000388 AC: 59AN: 152128Hom.: 1 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74380
ClinVar
Submissions by phenotype
Hypoplastic enamel-onycholysis-hypohidrosis syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at