rs79213434
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004527.4(MEOX1):c.11C>T(p.Ala4Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 1,564,174 control chromosomes in the GnomAD database, including 29 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 (★★). Synonymous variant affecting the same amino acid position (i.e. A4A) has been classified as Likely benign.
Frequency
Consequence
NM_004527.4 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 |
---|---|---|---|---|---|---|---|
MEOX1 | NM_004527.4 | c.11C>T | p.Ala4Val | missense_variant | 1/3 | ENST00000318579.9 | |
MEOX1 | NM_013999.4 | c.11C>T | p.Ala4Val | missense_variant | 1/2 | ||
MEOX1 | XM_011524818.3 | c.11C>T | p.Ala4Val | missense_variant | 1/3 | ||
MEOX1 | NM_001040002.2 | c.-204-131C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEOX1 | ENST00000318579.9 | c.11C>T | p.Ala4Val | missense_variant | 1/3 | 1 | NM_004527.4 | P1 | |
MEOX1 | ENST00000549132.2 | c.11C>T | p.Ala4Val | missense_variant | 1/2 | 1 | |||
MEOX1 | ENST00000393661.2 | c.-204-131C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00758 AC: 1152AN: 152058Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.00191 AC: 372AN: 194438Hom.: 1 AF XY: 0.00151 AC XY: 161AN XY: 106648
GnomAD4 exome AF: 0.000719 AC: 1015AN: 1411998Hom.: 14 Cov.: 35 AF XY: 0.000611 AC XY: 426AN XY: 697580
GnomAD4 genome AF: 0.00760 AC: 1157AN: 152176Hom.: 15 Cov.: 32 AF XY: 0.00735 AC XY: 547AN XY: 74414
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at