NM_177398.4:c.263+12127G>T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_177398.4(LMX1A):c.263+12127G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 152,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_177398.4 intron
Scores
Clinical Significance
Conservation
Publications
- autosomal dominant nonsyndromic hearing loss 7Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia
- Mobius syndromeInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- hearing loss, autosomal recessiveInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMX1A | NM_177398.4 | c.263+12127G>T | intron_variant | Intron 3 of 8 | ENST00000342310.7 | NP_796372.1 | ||
LMX1A | NM_001174069.2 | c.263+12127G>T | intron_variant | Intron 3 of 8 | NP_001167540.1 | |||
LMX1A | XM_011509540.3 | c.263+12127G>T | intron_variant | Intron 3 of 7 | XP_011507842.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMX1A | ENST00000342310.7 | c.263+12127G>T | intron_variant | Intron 3 of 8 | 2 | NM_177398.4 | ENSP00000340226.3 | |||
LMX1A | ENST00000367893.4 | c.263+12127G>T | intron_variant | Intron 2 of 7 | 1 | ENSP00000356868.4 | ||||
LMX1A | ENST00000294816.6 | c.263+12127G>T | intron_variant | Intron 3 of 8 | 2 | ENSP00000294816.2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152068Hom.: 0 Cov.: 30 show subpopulations
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152068Hom.: 0 Cov.: 30 AF XY: 0.0000269 AC XY: 2AN XY: 74274 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at