X-136548751-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_016267.4(VGLL1):c.377G>A(p.Arg126Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000463 in 1,210,430 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 201 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_016267.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VGLL1 | NM_016267.4 | c.377G>A | p.Arg126Gln | missense_variant | 3/5 | ENST00000370634.8 | NP_057351.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VGLL1 | ENST00000370634.8 | c.377G>A | p.Arg126Gln | missense_variant | 3/5 | 1 | NM_016267.4 | ENSP00000359668 | P1 | |
VGLL1 | ENST00000440515.5 | c.272G>A | p.Arg91Gln | missense_variant | 2/4 | 3 | ENSP00000398360 | |||
VGLL1 | ENST00000456412.1 | c.41-2017G>A | intron_variant | 3 | ENSP00000388868 |
Frequencies
GnomAD3 genomes AF: 0.000740 AC: 83AN: 112115Hom.: 0 Cov.: 23 AF XY: 0.000671 AC XY: 23AN XY: 34289
GnomAD3 exomes AF: 0.000545 AC: 100AN: 183435Hom.: 0 AF XY: 0.000633 AC XY: 43AN XY: 67885
GnomAD4 exome AF: 0.000435 AC: 478AN: 1098262Hom.: 0 Cov.: 32 AF XY: 0.000490 AC XY: 178AN XY: 363616
GnomAD4 genome AF: 0.000740 AC: 83AN: 112168Hom.: 0 Cov.: 23 AF XY: 0.000670 AC XY: 23AN XY: 34352
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at