chr20-62309415-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005560.6(LAMA5):c.11009T>C(p.Val3670Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000279 in 1,432,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005560.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA5 | NM_005560.6 | c.11009T>C | p.Val3670Ala | missense_variant | 80/80 | ENST00000252999.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA5 | ENST00000252999.7 | c.11009T>C | p.Val3670Ala | missense_variant | 80/80 | 1 | NM_005560.6 | P1 | |
LAMA5 | ENST00000370691.6 | n.2804T>C | non_coding_transcript_exon_variant | 17/17 | 1 | ||||
LAMA5 | ENST00000495695.1 | n.510T>C | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 exomes AF: 0.00000987 AC: 2AN: 202630Hom.: 0 AF XY: 0.00000894 AC XY: 1AN XY: 111918
GnomAD4 exome AF: 0.00000279 AC: 4AN: 1432166Hom.: 0 Cov.: 32 AF XY: 0.00000281 AC XY: 2AN XY: 711394
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.11009T>C (p.V3670A) alteration is located in exon 80 (coding exon 80) of the LAMA5 gene. This alteration results from a T to C substitution at nucleotide position 11009, causing the valine (V) at amino acid position 3670 to be replaced by an alanine (A). 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