chr1-226223830-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031944.3(MIXL1):c.149C>T(p.Ala50Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,210,668 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 Uncertain significance (★).
Frequency
Consequence
NM_031944.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIXL1 | NM_031944.3 | c.149C>T | p.Ala50Val | missense_variant | Exon 1 of 2 | ENST00000366810.6 | NP_114150.1 | |
MIXL1 | NM_001282402.2 | c.149C>T | p.Ala50Val | missense_variant | Exon 1 of 2 | NP_001269331.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000526 AC: 79AN: 150254Hom.: 1 Cov.: 32
GnomAD4 exome AF: 0.0000528 AC: 56AN: 1060306Hom.: 0 Cov.: 32 AF XY: 0.0000435 AC XY: 22AN XY: 506078
GnomAD4 genome AF: 0.000525 AC: 79AN: 150362Hom.: 1 Cov.: 32 AF XY: 0.000476 AC XY: 35AN XY: 73456
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.149C>T (p.A50V) alteration is located in exon 1 (coding exon 1) of the MIXL1 gene. This alteration results from a C to T substitution at nucleotide position 149, causing the alanine (A) at amino acid position 50 to be replaced by a valine (V). 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