17-38914462-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_006148.4(LASP1):c.495G>A(p.Pro165=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000061 in 1,606,460 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000056 ( 2 hom. )
Consequence
LASP1
NM_006148.4 synonymous
NM_006148.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.964
Genes affected
LASP1 (HGNC:6513): (LIM and SH3 protein 1) This gene encodes a member of a subfamily of LIM proteins, characterized by a LIM motif and a domain of Src homology region 3, and also a member of the nebulin family of actin-binding proteins. The encoded protein is a cAMP and cGMP dependent signaling protein and binds to the actin cytoskeleton at extensions of the cell membrane. The encoded protein has been linked to metastatic breast cancer, hematopoetic tumors such as B-cell lymphomas, and colorectal cancer. [provided by RefSeq, Oct 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 17-38914462-G-A is Benign according to our data. Variant chr17-38914462-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 745719.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.964 with no splicing effect.
BS2
High AC in GnomAd4 at 17 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LASP1 | NM_006148.4 | c.495G>A | p.Pro165= | synonymous_variant | 5/7 | ENST00000318008.11 | NP_006139.1 | |
LASP1 | NM_001271608.2 | c.327G>A | p.Pro109= | synonymous_variant | 4/6 | NP_001258537.1 | ||
LASP1 | XM_047435965.1 | c.387G>A | p.Pro129= | synonymous_variant | 5/7 | XP_047291921.1 | ||
LASP1 | NR_073384.2 | n.797G>A | non_coding_transcript_exon_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LASP1 | ENST00000318008.11 | c.495G>A | p.Pro165= | synonymous_variant | 5/7 | 1 | NM_006148.4 | ENSP00000325240 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152168Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000256 AC: 62AN: 242412Hom.: 1 AF XY: 0.000236 AC XY: 31AN XY: 131324
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GnomAD4 exome AF: 0.0000557 AC: 81AN: 1454174Hom.: 2 Cov.: 63 AF XY: 0.0000512 AC XY: 37AN XY: 723042
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GnomAD4 genome AF: 0.000112 AC: 17AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74470
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 31, 2018 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at