rs565429072
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000426.4(LAMA2):āc.5382A>Gā(p.Thr1794=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000892 in 1,614,124 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. T1794T) has been classified as Benign.
Frequency
Consequence
NM_000426.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.5382A>G | p.Thr1794= | synonymous_variant | 37/65 | ENST00000421865.3 | NP_000417.3 | |
LAMA2 | NM_001079823.2 | c.5382A>G | p.Thr1794= | synonymous_variant | 37/64 | NP_001073291.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.5382A>G | p.Thr1794= | synonymous_variant | 37/65 | 5 | NM_000426.4 | ENSP00000400365 | ||
LAMA2 | ENST00000618192.5 | c.5646A>G | p.Thr1882= | synonymous_variant | 38/66 | 5 | ENSP00000480802 | P1 | ||
LAMA2 | ENST00000617695.5 | c.5382A>G | p.Thr1794= | synonymous_variant | 37/64 | 5 | ENSP00000481744 | |||
LAMA2 | ENST00000687590.1 | n.1802A>G | non_coding_transcript_exon_variant | 5/5 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251360Hom.: 1 AF XY: 0.000228 AC XY: 31AN XY: 135834
GnomAD4 exome AF: 0.0000951 AC: 139AN: 1461782Hom.: 1 Cov.: 31 AF XY: 0.000131 AC XY: 95AN XY: 727200
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74500
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 09, 2016 | - - |
LAMA2-related muscular dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 20, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | LAMA2: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at