chr4-176684029-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005429.5(VEGFC):c.1157G>A(p.Arg386Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000062 in 1,613,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R386W) has been classified as Likely benign.
Frequency
Consequence
NM_005429.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VEGFC | NM_005429.5 | c.1157G>A | p.Arg386Gln | missense_variant | 7/7 | ENST00000618562.2 | |
HAFML | NR_183975.1 | n.182+14320C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VEGFC | ENST00000618562.2 | c.1157G>A | p.Arg386Gln | missense_variant | 7/7 | 1 | NM_005429.5 | P1 | |
HAFML | ENST00000509194.1 | n.89+14320C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
HAFML | ENST00000504017.5 | n.140+4279C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249032Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135158
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461618Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727146
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
VEGFC-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 23, 2024 | The VEGFC c.1157G>A variant is predicted to result in the amino acid substitution p.Arg386Gln. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0033% of alleles in individuals of South Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at