chr7-108024059-AT-A
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_007356.3(LAMB4):βc.5265delβ(p.Lys1755AsnfsTer11) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00973 in 1,607,420 control chromosomes in the GnomAD database, including 97 homozygotes. Variant has been reported in ClinVar as Benign (β ).
Frequency
Genomes: π 0.0064 ( 5 hom., cov: 33)
Exomes π: 0.010 ( 92 hom. )
Consequence
LAMB4
NM_007356.3 frameshift
NM_007356.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.633
Genes affected
LAMB4 (HGNC:6491): (laminin subunit beta 4) Predicted to be an extracellular matrix structural constituent. Predicted to be involved in several processes, including basement membrane assembly; cell migration; and substrate adhesion-dependent cell spreading. Predicted to be located in basement membrane; extracellular region; and membrane. Predicted to be part of laminin complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM4
Frameshift in the end of transcript resulting in stoplost. Downstream stopcodon found after 1760 codons.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMB4 | NM_007356.3 | c.5265del | p.Lys1755AsnfsTer11 | frameshift_variant | 34/34 | ENST00000388781.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMB4 | ENST00000388781.8 | c.5265del | p.Lys1755AsnfsTer11 | frameshift_variant | 34/34 | 1 | NM_007356.3 | P1 | |
LAMB4 | ENST00000205386.8 | c.5265del | p.Lys1755AsnfsTer11 | frameshift_variant | 34/34 | 1 | P1 | ||
LAMB4 | ENST00000483484.5 | n.487del | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00638 AC: 970AN: 151992Hom.: 5 Cov.: 33
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GnomAD3 exomes AF: 0.00741 AC: 1756AN: 236956Hom.: 18 AF XY: 0.00731 AC XY: 937AN XY: 128148
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GnomAD4 exome AF: 0.0101 AC: 14675AN: 1455310Hom.: 92 Cov.: 29 AF XY: 0.00993 AC XY: 7188AN XY: 723786
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GnomAD4 genome AF: 0.00638 AC: 970AN: 152110Hom.: 5 Cov.: 33 AF XY: 0.00604 AC XY: 449AN XY: 74374
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at