chr10-76047256-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_001305581.2(LRMDA):c.351C>A(p.Asn117Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,666 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Synonymous variant affecting the same amino acid position (i.e. N117N) has been classified as Likely benign.
Frequency
Consequence
NM_001305581.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRMDA | NM_001305581.2 | c.351C>A | p.Asn117Lys | missense_variant | 4/7 | ENST00000611255.5 | |
LRMDA | NM_032024.5 | c.267C>A | p.Asn89Lys | missense_variant | 3/6 | ||
LRMDA | NR_131178.2 | n.705C>A | non_coding_transcript_exon_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRMDA | ENST00000611255.5 | c.351C>A | p.Asn117Lys | missense_variant | 4/7 | 5 | NM_001305581.2 | P1 | |
LRMDA | ENST00000372499.5 | c.267C>A | p.Asn89Lys | missense_variant | 3/6 | 1 | |||
LRMDA | ENST00000593699.5 | n.705C>A | non_coding_transcript_exon_variant | 5/8 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461666Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727134
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Oculocutaneous albinism type 7 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Science and Research Branch, Islamic Azad University, Islamic Azad University | Aug 05, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at