chr7-73596417-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032951.3(MLXIPL):c.1885C>T(p.Arg629Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,612,700 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032951.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLXIPL | NM_032951.3 | c.1885C>T | p.Arg629Cys | missense_variant | 12/17 | ENST00000313375.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLXIPL | ENST00000313375.8 | c.1885C>T | p.Arg629Cys | missense_variant | 12/17 | 1 | NM_032951.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151886Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249474Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135402
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460814Hom.: 0 Cov.: 36 AF XY: 0.0000138 AC XY: 10AN XY: 726728
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 151886Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74150
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.1885C>T (p.R629C) alteration is located in exon 12 (coding exon 12) of the MLXIPL gene. This alteration results from a C to T substitution at nucleotide position 1885, causing the arginine (R) at amino acid position 629 to be replaced by a cysteine (C). 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