chr1-115651423-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_138959.3(VANGL1):c.10G>A(p.Glu4Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,613,760 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138959.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VANGL1 | NM_138959.3 | c.10G>A | p.Glu4Lys | missense_variant | Exon 2 of 8 | ENST00000355485.7 | NP_620409.1 | |
VANGL1 | NM_001172412.2 | c.10G>A | p.Glu4Lys | missense_variant | Exon 2 of 8 | NP_001165883.1 | ||
VANGL1 | NM_001172411.2 | c.10G>A | p.Glu4Lys | missense_variant | Exon 2 of 8 | NP_001165882.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VANGL1 | ENST00000355485.7 | c.10G>A | p.Glu4Lys | missense_variant | Exon 2 of 8 | 1 | NM_138959.3 | ENSP00000347672.2 | ||
VANGL1 | ENST00000310260.7 | c.10G>A | p.Glu4Lys | missense_variant | Exon 2 of 8 | 1 | ENSP00000310800.3 | |||
VANGL1 | ENST00000369509.1 | c.10G>A | p.Glu4Lys | missense_variant | Exon 1 of 7 | 1 | ENSP00000358522.1 | |||
VANGL1 | ENST00000369510.8 | c.10G>A | p.Glu4Lys | missense_variant | Exon 2 of 8 | 1 | ENSP00000358523.3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251282Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135834
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461652Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 727136
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74312
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.10G>A (p.E4K) alteration is located in exon 2 (coding exon 1) of the VANGL1 gene. This alteration results from a G to A substitution at nucleotide position 10, causing the glutamic acid (E) at amino acid position 4 to be replaced by a lysine (K). 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