rs566655
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005559.4(LAMA1):āc.2021A>Cā(p.Asn674Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,613,588 control chromosomes in the GnomAD database, including 38,064 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. N674N) has been classified as Likely benign.
Frequency
Consequence
NM_005559.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA1 | NM_005559.4 | c.2021A>C | p.Asn674Thr | missense_variant | 14/63 | ENST00000389658.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA1 | ENST00000389658.4 | c.2021A>C | p.Asn674Thr | missense_variant | 14/63 | 1 | NM_005559.4 | P1 | |
LAMA1 | ENST00000579014.5 | n.3036A>C | non_coding_transcript_exon_variant | 13/62 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.200 AC: 30412AN: 152002Hom.: 3228 Cov.: 33
GnomAD3 exomes AF: 0.197 AC: 49418AN: 251384Hom.: 5325 AF XY: 0.198 AC XY: 26970AN XY: 135872
GnomAD4 exome AF: 0.214 AC: 313395AN: 1461468Hom.: 34828 Cov.: 34 AF XY: 0.213 AC XY: 155145AN XY: 727072
GnomAD4 genome ? AF: 0.200 AC: 30438AN: 152120Hom.: 3236 Cov.: 33 AF XY: 0.199 AC XY: 14763AN XY: 74352
ClinVar
Submissions by phenotype
Ataxia - intellectual disability - oculomotor apraxia - cerebellar cysts syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 13, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at