rs141673853
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_138959.3(VANGL1):āc.323A>Gā(p.Lys108Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 1,614,166 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_138959.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VANGL1 | NM_138959.3 | c.323A>G | p.Lys108Arg | missense_variant | 4/8 | ENST00000355485.7 | |
VANGL1 | NM_001172412.2 | c.323A>G | p.Lys108Arg | missense_variant | 4/8 | ||
VANGL1 | NM_001172411.2 | c.317A>G | p.Lys106Arg | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VANGL1 | ENST00000355485.7 | c.323A>G | p.Lys108Arg | missense_variant | 4/8 | 1 | NM_138959.3 | P3 | |
VANGL1 | ENST00000310260.7 | c.323A>G | p.Lys108Arg | missense_variant | 4/8 | 1 | P3 | ||
VANGL1 | ENST00000369509.1 | c.323A>G | p.Lys108Arg | missense_variant | 3/7 | 1 | P3 | ||
VANGL1 | ENST00000369510.8 | c.317A>G | p.Lys106Arg | missense_variant | 4/8 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00160 AC: 244AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000895 AC: 225AN: 251494Hom.: 1 AF XY: 0.000949 AC XY: 129AN XY: 135920
GnomAD4 exome AF: 0.00136 AC: 1995AN: 1461894Hom.: 4 Cov.: 31 AF XY: 0.00136 AC XY: 989AN XY: 727248
GnomAD4 genome ? AF: 0.00160 AC: 244AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.00162 AC XY: 121AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 08, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | VANGL1: BS1, BS2 - |
Sacral defect with anterior meningocele Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Neural tube defect Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at