rs397517864
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001384474.1(LOXHD1):c.6050-15C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,547,414 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001384474.1 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.6050-15C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000642948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.6050-15C>T | splice_polypyrimidine_tract_variant, intron_variant | NM_001384474.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000532 AC: 8AN: 150466Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000190 AC: 30AN: 157968Hom.: 0 AF XY: 0.000240 AC XY: 20AN XY: 83380
GnomAD4 exome AF: 0.000112 AC: 156AN: 1396830Hom.: 0 Cov.: 35 AF XY: 0.000123 AC XY: 85AN XY: 688404
GnomAD4 genome AF: 0.0000531 AC: 8AN: 150584Hom.: 0 Cov.: 30 AF XY: 0.0000681 AC XY: 5AN XY: 73418
ClinVar
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 77 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | May 23, 2017 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 06, 2013 | 5864-15C>T intron 37 in LOXHD1: This variant is not expected to have clinical si gnificance because it is not located within the splice consensus sequence. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at