chr7-108047994-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007356.3(LAMB4):c.4240C>T(p.Leu1414Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007356.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMB4 | NM_007356.3 | c.4240C>T | p.Leu1414Phe | missense_variant | 28/34 | ENST00000388781.8 | |
LOC107986835 | XR_001745320.1 | n.658+560G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMB4 | ENST00000388781.8 | c.4240C>T | p.Leu1414Phe | missense_variant | 28/34 | 1 | NM_007356.3 | P1 | |
LAMB4 | ENST00000205386.8 | c.4240C>T | p.Leu1414Phe | missense_variant | 28/34 | 1 | P1 | ||
LAMB4 | ENST00000422975.1 | c.1318C>T | p.Leu440Phe | missense_variant | 7/13 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251444Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135902
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461862Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727238
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.4240C>T (p.L1414F) alteration is located in exon 28 (coding exon 27) of the LAMB4 gene. This alteration results from a C to T substitution at nucleotide position 4240, causing the leucine (L) at amino acid position 1414 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at