2-210441411-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006055.3(LANCL1):c.440C>A(p.Ala147Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000202 in 1,611,292 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006055.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LANCL1 | NM_006055.3 | c.440C>A | p.Ala147Asp | missense_variant | 5/10 | ENST00000450366.7 | NP_006046.1 | |
LANCL1-AS1 | NR_110604.1 | n.211-1131G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LANCL1 | ENST00000450366.7 | c.440C>A | p.Ala147Asp | missense_variant | 5/10 | 1 | NM_006055.3 | ENSP00000393597 | P1 | |
LANCL1-AS1 | ENST00000420418.5 | n.157-1131G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152104Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 250936Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135636
GnomAD4 exome AF: 0.000211 AC: 308AN: 1459188Hom.: 0 Cov.: 30 AF XY: 0.000218 AC XY: 158AN XY: 725884
GnomAD4 genome AF: 0.000118 AC: 18AN: 152104Hom.: 1 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.440C>A (p.A147D) alteration is located in exon 5 (coding exon 4) of the LANCL1 gene. This alteration results from a C to A substitution at nucleotide position 440, causing the alanine (A) at amino acid position 147 to be replaced by an aspartic acid (D). 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