7-108043829-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_007356.3(LAMB4):c.4394G>T(p.Gly1465Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,607,940 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 42 hom., cov: 31)
Exomes 𝑓: 0.0014 ( 34 hom. )
Consequence
LAMB4
NM_007356.3 missense
NM_007356.3 missense
Scores
1
16
Clinical Significance
Conservation
PhyloP100: 0.704
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 Benign. Variant got -10 ACMG points.
BP6
?
Variant 7-108043829-C-A is Benign according to our data. Variant chr7-108043829-C-A is described in ClinVar as [Benign]. Clinvar id is 768193.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0121 (1837/152020) while in subpopulation AFR AF= 0.0416 (1728/41490). AF 95% confidence interval is 0.04. There are 42 homozygotes in gnomad4. There are 883 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 43 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMB4 | NM_007356.3 | c.4394G>T | p.Gly1465Val | missense_variant | 29/34 | ENST00000388781.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMB4 | ENST00000388781.8 | c.4394G>T | p.Gly1465Val | missense_variant | 29/34 | 1 | NM_007356.3 | P1 | |
LAMB4 | ENST00000205386.8 | c.4394G>T | p.Gly1465Val | missense_variant | 29/34 | 1 | P1 | ||
LAMB4 | ENST00000422975.1 | c.1472G>T | p.Gly491Val | missense_variant | 8/13 | 1 | |||
LAMB4 | ENST00000475572.1 | n.95G>T | non_coding_transcript_exon_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0121 AC: 1839AN: 151902Hom.: 43 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00349 AC: 862AN: 246994Hom.: 17 AF XY: 0.00250 AC XY: 334AN XY: 133630
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GnomAD4 exome AF: 0.00140 AC: 2040AN: 1455920Hom.: 34 Cov.: 29 AF XY: 0.00121 AC XY: 878AN XY: 724318
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GnomAD4 genome ? AF: 0.0121 AC: 1837AN: 152020Hom.: 42 Cov.: 31 AF XY: 0.0119 AC XY: 883AN XY: 74306
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ESP6500AA
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ExAC
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495
Asia WGS
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3476
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 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;D
REVEL
Benign
Sift
Uncertain
D;D;T
Sift4G
Benign
T;T;T
Polyphen
B;B;.
Vest4
MVP
MPC
0.085
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at