rs727503144
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001384474.1(LOXHD1):c.3162G>A(p.Thr1054=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000271 in 1,399,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T1054T) has been classified as Likely benign.
Frequency
Consequence
NM_001384474.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.3162G>A | p.Thr1054= | synonymous_variant | 20/41 | ENST00000642948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.3162G>A | p.Thr1054= | synonymous_variant | 20/41 | NM_001384474.1 | P1 | ||
LOXHD1 | ENST00000536736.5 | c.3162G>A | p.Thr1054= | synonymous_variant | 20/40 | 5 | |||
LOXHD1 | ENST00000441551.6 | c.2599-2013G>A | intron_variant | 5 | |||||
LOXHD1 | ENST00000335730.6 | n.2475G>A | non_coding_transcript_exon_variant | 13/27 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000250 AC: 4AN: 159840Hom.: 0 AF XY: 0.0000119 AC XY: 1AN XY: 83944
GnomAD4 exome AF: 0.0000271 AC: 38AN: 1399796Hom.: 0 Cov.: 32 AF XY: 0.0000246 AC XY: 17AN XY: 690396
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 05, 2014 | Thr1054Thr in exon 20 of LOXHD1: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. - |
Autosomal recessive nonsyndromic hearing loss 77 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Counsyl | Jun 29, 2017 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 07, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at