NM_198129.4:c.374G>A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_198129.4(LAMA3):c.374G>A(p.Arg125His) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,613,532 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 Uncertain significance (★).
Frequency
Consequence
NM_198129.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA3 | ENST00000313654.14 | c.374G>A | p.Arg125His | missense_variant | Exon 2 of 75 | 1 | NM_198129.4 | ENSP00000324532.8 | ||
LAMA3 | ENST00000399516.7 | c.374G>A | p.Arg125His | missense_variant | Exon 2 of 74 | 1 | ENSP00000382432.2 | |||
LAMA3 | ENST00000585600.5 | n.374G>A | non_coding_transcript_exon_variant | Exon 2 of 13 | 1 | ENSP00000468316.1 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151656Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000601 AC: 15AN: 249516Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135370
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461760Hom.: 0 Cov.: 34 AF XY: 0.00000963 AC XY: 7AN XY: 727206
GnomAD4 genome AF: 0.0000264 AC: 4AN: 151772Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2AN XY: 74148
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.374G>A (p.R125H) alteration is located in exon 2 (coding exon 2) of the LAMA3 gene. This alteration results from a G to A substitution at nucleotide position 374, causing the arginine (R) at amino acid position 125 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at