17-38915129-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006148.4(LASP1):c.595G>A(p.Ala199Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,686 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_006148.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LASP1 | NM_006148.4 | c.595G>A | p.Ala199Thr | missense_variant | 6/7 | ENST00000318008.11 | |
LASP1 | NM_001271608.2 | c.427G>A | p.Ala143Thr | missense_variant | 5/6 | ||
LASP1 | XM_047435965.1 | c.487G>A | p.Ala163Thr | missense_variant | 6/7 | ||
LASP1 | NR_073384.2 | n.897G>A | non_coding_transcript_exon_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LASP1 | ENST00000318008.11 | c.595G>A | p.Ala199Thr | missense_variant | 6/7 | 1 | NM_006148.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152056Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250188Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135318
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461630Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727112
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152056Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.595G>A (p.A199T) alteration is located in exon 6 (coding exon 6) of the LASP1 gene. This alteration results from a G to A substitution at nucleotide position 595, causing the alanine (A) at amino acid position 199 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