chr2-210455267-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006055.3(LANCL1):c.247G>A(p.Ala83Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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.247G>A | p.Ala83Thr | missense_variant | 4/10 | ENST00000450366.7 | NP_006046.1 | |
LANCL1-AS1 | NR_110604.1 | n.369-5208C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LANCL1 | ENST00000450366.7 | c.247G>A | p.Ala83Thr | missense_variant | 4/10 | 1 | NM_006055.3 | ENSP00000393597 | P1 | |
LANCL1-AS1 | ENST00000420418.5 | n.315-5208C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250984Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135640
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461062Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1AN XY: 726858
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2022 | The c.247G>A (p.A83T) alteration is located in exon 4 (coding exon 3) of the LANCL1 gene. This alteration results from a G to A substitution at nucleotide position 247, causing the alanine (A) at amino acid position 83 to be replaced by a threonine (T). 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