chr5-122077761-G-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002317.7(LOX):c.225C>A(p.Ala75=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000428 in 1,400,576 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. A75A) has been classified as Benign.
Frequency
Consequence
NM_002317.7 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 |
---|---|---|---|---|---|---|---|
LOX | NM_002317.7 | c.225C>A | p.Ala75= | synonymous_variant | 1/7 | ENST00000231004.5 | |
SRFBP1 | XM_017009111.3 | c.*2436G>T | 3_prime_UTR_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOX | ENST00000231004.5 | c.225C>A | p.Ala75= | synonymous_variant | 1/7 | 1 | NM_002317.7 | P1 | |
LOX | ENST00000639739.2 | c.225C>A | p.Ala75= | synonymous_variant, NMD_transcript_variant | 1/6 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000205 AC: 3AN: 146686Hom.: 0 AF XY: 0.0000124 AC XY: 1AN XY: 80802
GnomAD4 exome AF: 0.00000428 AC: 6AN: 1400576Hom.: 0 Cov.: 33 AF XY: 0.00000433 AC XY: 3AN XY: 692448
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at