6-129512482-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_000426.4(LAMA2):āc.8977A>Gā(p.Ile2993Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000514 in 1,613,564 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000426.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.8977A>G | p.Ile2993Val | missense_variant | 63/65 | ENST00000421865.3 | NP_000417.3 | |
LOC102723409 | XR_001743860.2 | n.12103-9691T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.8977A>G | p.Ile2993Val | missense_variant | 63/65 | 5 | NM_000426.4 | ENSP00000400365 | ||
ENST00000665046.1 | n.789-9691T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251236Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135762
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461328Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 726988
GnomAD4 genome AF: 0.000322 AC: 49AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74430
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 03, 2019 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.8977A>G (p.I2993V) alteration is located in exon 63 (coding exon 63) of the LAMA2 gene. This alteration results from a A to G substitution at nucleotide position 8977, causing the isoleucine (I) at amino acid position 2993 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
LAMA2-related muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at