rs117096733
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000426.4(LAMA2):c.2857-39T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0142 in 1,598,178 control chromosomes in the GnomAD database, including 205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_000426.4 intron
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 |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.2857-39T>C | intron_variant | ENST00000421865.3 | |||
LAMA2 | NM_001079823.2 | c.2857-39T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.2857-39T>C | intron_variant | 5 | NM_000426.4 | ||||
LAMA2 | ENST00000617695.5 | c.2857-39T>C | intron_variant | 5 | |||||
LAMA2 | ENST00000618192.5 | c.3121-39T>C | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0103 AC: 1562AN: 152192Hom.: 11 Cov.: 33
GnomAD3 exomes AF: 0.0108 AC: 2704AN: 249598Hom.: 20 AF XY: 0.0110 AC XY: 1487AN XY: 134974
GnomAD4 exome AF: 0.0146 AC: 21128AN: 1445868Hom.: 194 Cov.: 29 AF XY: 0.0146 AC XY: 10517AN XY: 720248
GnomAD4 genome ? AF: 0.0103 AC: 1565AN: 152310Hom.: 11 Cov.: 33 AF XY: 0.00976 AC XY: 727AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 11, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at