18-6942239-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005559.4(LAMA1):c.9068C>A(p.Ala3023Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict 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 Uncertain significance (★).
Frequency
Consequence
NM_005559.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMA1 | NM_005559.4 | c.9068C>A | p.Ala3023Asp | missense_variant, splice_region_variant | 63/63 | ENST00000389658.4 | NP_005550.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA1 | ENST00000389658.4 | c.9068C>A | p.Ala3023Asp | missense_variant, splice_region_variant | 63/63 | 1 | NM_005559.4 | ENSP00000374309 | P1 | |
LAMA1 | ENST00000488064.5 | n.2475C>A | splice_region_variant, non_coding_transcript_exon_variant | 14/14 | 2 | |||||
LAMA1 | ENST00000492048.5 | n.1956C>A | splice_region_variant, non_coding_transcript_exon_variant | 7/7 | 2 | |||||
LAMA1 | ENST00000579014.5 | n.10083C>A | splice_region_variant, non_coding_transcript_exon_variant | 62/62 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248608Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134634
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461664Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727132
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74450
ClinVar
Submissions by phenotype
Ataxia - intellectual disability - oculomotor apraxia - cerebellar cysts syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Feb 06, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at