rs75992359
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000431543.6(LAMA4):c.368G>A(p.Arg123Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00679 in 758,944 control chromosomes in the GnomAD database, including 131 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000431543.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMA4 | NM_001105206.3 | c.297+2368G>A | intron_variant | ENST00000230538.12 | NP_001098676.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA4 | ENST00000230538.12 | c.297+2368G>A | intron_variant | 1 | NM_001105206.3 | ENSP00000230538.7 |
Frequencies
GnomAD3 genomes AF: 0.0194 AC: 2948AN: 152138Hom.: 88 Cov.: 32
GnomAD3 exomes AF: 0.00553 AC: 1279AN: 231458Hom.: 29 AF XY: 0.00460 AC XY: 587AN XY: 127744
GnomAD4 exome AF: 0.00361 AC: 2192AN: 606688Hom.: 42 Cov.: 0 AF XY: 0.00299 AC XY: 991AN XY: 331970
GnomAD4 genome AF: 0.0194 AC: 2960AN: 152256Hom.: 89 Cov.: 32 AF XY: 0.0186 AC XY: 1382AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | research | Biesecker Lab/Clinical Genomics Section, National Institutes of Health | Jun 24, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at