chr6-129475381-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000426.4(LAMA2):c.7440-9G>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000697 in 143,408 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000426.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.7440-9G>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000421865.3 | |||
LAMA2 | NM_001079823.2 | c.7439+2029G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.7440-9G>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_000426.4 | ||||
ENST00000665046.1 | n.975+27224C>G | intron_variant, non_coding_transcript_variant | |||||||
LAMA2 | ENST00000617695.5 | c.7439+2029G>C | intron_variant | 5 | |||||
LAMA2 | ENST00000618192.5 | c.7704-9G>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000697 AC: 1AN: 143408Hom.: 0 Cov.: 28
GnomAD4 exome Cov.: 21
GnomAD4 genome AF: 0.00000697 AC: 1AN: 143408Hom.: 0 Cov.: 28 AF XY: 0.0000144 AC XY: 1AN XY: 69262
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at