rs774472247
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_ModeratePM2PP3_StrongPP5_Moderate
The NM_000228.3(LAMB3):c.3052-1G>A variant causes a splice acceptor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_000228.3 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMB3 | NM_000228.3 | c.3052-1G>A | splice_acceptor_variant | ENST00000356082.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMB3 | ENST00000356082.9 | c.3052-1G>A | splice_acceptor_variant | 1 | NM_000228.3 | P1 | |||
LAMB3 | ENST00000367030.7 | c.3052-1G>A | splice_acceptor_variant | 1 | P1 | ||||
LAMB3 | ENST00000391911.5 | c.3052-1G>A | splice_acceptor_variant | 1 | P1 | ||||
LAMB3 | ENST00000455193.1 | c.259-1G>A | splice_acceptor_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251020Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135676
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461478Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727038
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Junctional epidermolysis bullosa gravis of Herlitz Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Apr 07, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at