chr1-160419532-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020335.3(VANGL2):c.723G>T(p.Gln241His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000418 in 1,601,230 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_020335.3 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 |
---|---|---|---|---|---|---|---|
VANGL2 | NM_020335.3 | c.723G>T | p.Gln241His | missense_variant | 4/8 | ENST00000368061.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VANGL2 | ENST00000368061.3 | c.723G>T | p.Gln241His | missense_variant | 4/8 | 2 | NM_020335.3 | P1 | |
VANGL2 | ENST00000696602.1 | c.867G>T | p.Gln289His | missense_variant | 4/8 | ||||
VANGL2 | ENST00000483408.1 | n.40G>T | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152202Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000541 AC: 13AN: 240402Hom.: 0 AF XY: 0.0000229 AC XY: 3AN XY: 130844
GnomAD4 exome AF: 0.0000290 AC: 42AN: 1448910Hom.: 0 Cov.: 32 AF XY: 0.0000277 AC XY: 20AN XY: 721242
GnomAD4 genome AF: 0.000164 AC: 25AN: 152320Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74476
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2022 | The c.723G>T (p.Q241H) alteration is located in exon 4 (coding exon 3) of the VANGL2 gene. This alteration results from a G to T substitution at nucleotide position 723, causing the glutamine (Q) at amino acid position 241 to be replaced by a histidine (H). 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