rs764128579
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001384474.1(LOXHD1):c.3061+8G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,539,532 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001384474.1 splice_region, 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.3061+8G>T | splice_region_variant, intron_variant | ENST00000642948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.3061+8G>T | splice_region_variant, intron_variant | NM_001384474.1 | P1 | ||||
LOXHD1 | ENST00000441551.6 | c.2599-2586G>T | intron_variant | 5 | |||||
LOXHD1 | ENST00000536736.5 | c.3061+8G>T | splice_region_variant, intron_variant | 5 | |||||
LOXHD1 | ENST00000335730.6 | n.2374+8G>T | splice_region_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000331 AC: 5AN: 151170Hom.: 0 Cov.: 27
GnomAD3 exomes AF: 0.0000194 AC: 3AN: 154340Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 81628
GnomAD4 exome AF: 0.0000720 AC: 100AN: 1388362Hom.: 0 Cov.: 36 AF XY: 0.0000644 AC XY: 44AN XY: 683124
GnomAD4 genome ? AF: 0.0000331 AC: 5AN: 151170Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 73784
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 03, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 25, 2016 | c.3061+8G>T in intron 19 of LOXHD1: This variant is not expected to have clinic al significance because it is not located within the splice consensus sequence. It has been identified in 2/6860 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs764128579). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at