rs4925386
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005560.6(LAMA5):c.1417+93A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 1,582,194 control chromosomes in the GnomAD database, including 354,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.56 ( 27142 hom., cov: 32)
Exomes 𝑓: 0.67 ( 327617 hom. )
Consequence
LAMA5
NM_005560.6 intron
NM_005560.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.579
Genes affected
LAMA5 (HGNC:6485): (laminin subunit alpha 5) This gene encodes one of the vertebrate laminin alpha chains. Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Laminins are composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively) and they form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene. The protein encoded by this gene is the alpha-5 subunit of of laminin-10 (laminin-511), laminin-11 (laminin-521) and laminin-15 (laminin-523). [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 20-62345988-T-C is Benign according to our data. Variant chr20-62345988-T-C is described in ClinVar as [Benign]. Clinvar id is 1297291.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMA5 | NM_005560.6 | c.1417+93A>G | intron_variant | ENST00000252999.7 | |||
LOC124904946 | XR_007067699.1 | n.389T>C | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMA5 | ENST00000252999.7 | c.1417+93A>G | intron_variant | 1 | NM_005560.6 | P1 | |||
LAMA5 | ENST00000370677.4 | n.1442+93A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.564 AC: 85738AN: 151944Hom.: 27139 Cov.: 32
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GnomAD4 exome AF: 0.672 AC: 961514AN: 1430132Hom.: 327617 Cov.: 27 AF XY: 0.672 AC XY: 476871AN XY: 709932
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GnomAD4 genome ? AF: 0.564 AC: 85758AN: 152062Hom.: 27142 Cov.: 32 AF XY: 0.567 AC XY: 42137AN XY: 74320
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | This variant is associated with the following publications: (PMID: 21761138) - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at