chrX-37667461-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001170331.2(LANCL3):c.1075A>G(p.Asn359Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000016 in 1,185,884 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001170331.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LANCL3 | NM_001170331.2 | c.1075A>G | p.Asn359Asp | missense_variant | 4/5 | ENST00000378619.4 | |
LANCL3 | NM_198511.3 | c.1075A>G | p.Asn359Asp | missense_variant | 4/6 | ||
LANCL3 | XM_011543904.3 | c.529A>G | p.Asn177Asp | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LANCL3 | ENST00000378619.4 | c.1075A>G | p.Asn359Asp | missense_variant | 4/5 | 1 | NM_001170331.2 | P1 | |
LANCL3 | ENST00000378621.7 | c.1075A>G | p.Asn359Asp | missense_variant | 4/6 | 1 | |||
LANCL3 | ENST00000614025.4 | c.1075A>G | p.Asn359Asp | missense_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000453 AC: 5AN: 110357Hom.: 0 Cov.: 22 AF XY: 0.0000611 AC XY: 2AN XY: 32719
GnomAD3 exomes AF: 0.0000190 AC: 3AN: 157484Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 48472
GnomAD4 exome AF: 0.0000130 AC: 14AN: 1075527Hom.: 0 Cov.: 29 AF XY: 0.00000866 AC XY: 3AN XY: 346619
GnomAD4 genome ? AF: 0.0000453 AC: 5AN: 110357Hom.: 0 Cov.: 22 AF XY: 0.0000611 AC XY: 2AN XY: 32719
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.1075A>G (p.N359D) alteration is located in exon 4 (coding exon 4) of the LANCL3 gene. This alteration results from a A to G substitution at nucleotide position 1075, causing the asparagine (N) at amino acid position 359 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