NM_198129.4:c.26G>A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198129.4(LAMA3):c.26G>A(p.Gly9Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA3 | ENST00000313654.14 | c.26G>A | p.Gly9Asp | missense_variant | Exon 1 of 75 | 1 | NM_198129.4 | ENSP00000324532.8 | ||
LAMA3 | ENST00000399516.7 | c.26G>A | p.Gly9Asp | missense_variant | Exon 1 of 74 | 1 | ENSP00000382432.2 | |||
LAMA3 | ENST00000585600.5 | n.26G>A | non_coding_transcript_exon_variant | Exon 1 of 13 | 1 | ENSP00000468316.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1210726Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 586212
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.26G>A (p.G9D) alteration is located in exon 1 (coding exon 1) of the LAMA3 gene. This alteration results from a G to A substitution at nucleotide position 26, causing the glycine (G) at amino acid position 9 to be replaced by an aspartic acid (D). 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