rs9898682
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004527.4(MEOX1):c.80C>T(p.Ser27Leu) variant causes a missense change. The variant allele was found at a frequency of 0.11 in 1,610,480 control chromosomes in the GnomAD database, including 12,211 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. S27S) has been classified as Likely benign.
Frequency
Consequence
NM_004527.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEOX1 | NM_004527.4 | c.80C>T | p.Ser27Leu | missense_variant | 1/3 | ENST00000318579.9 | |
MEOX1 | NM_013999.4 | c.80C>T | p.Ser27Leu | missense_variant | 1/2 | ||
MEOX1 | XM_011524818.3 | c.80C>T | p.Ser27Leu | missense_variant | 1/3 | ||
MEOX1 | NM_001040002.2 | c.-204-62C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEOX1 | ENST00000318579.9 | c.80C>T | p.Ser27Leu | missense_variant | 1/3 | 1 | NM_004527.4 | P1 | |
MEOX1 | ENST00000549132.2 | c.80C>T | p.Ser27Leu | missense_variant | 1/2 | 1 | |||
MEOX1 | ENST00000393661.2 | c.-204-62C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.160 AC: 24339AN: 151798Hom.: 2817 Cov.: 31
GnomAD3 exomes AF: 0.103 AC: 24847AN: 242056Hom.: 1884 AF XY: 0.101 AC XY: 13315AN XY: 131940
GnomAD4 exome AF: 0.104 AC: 152340AN: 1458564Hom.: 9389 Cov.: 36 AF XY: 0.104 AC XY: 75212AN XY: 725354
GnomAD4 genome AF: 0.160 AC: 24364AN: 151916Hom.: 2822 Cov.: 31 AF XY: 0.158 AC XY: 11701AN XY: 74266
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at