X-13603406-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015507.4(EGFL6):c.490C>T(p.Arg164Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00272 in 1,208,543 control chromosomes in the GnomAD database, including 66 homozygotes. There are 828 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_015507.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGFL6 | NM_015507.4 | c.490C>T | p.Arg164Cys | missense_variant | 5/12 | ENST00000361306.6 | |
EGFL6 | NM_001167890.2 | c.490C>T | p.Arg164Cys | missense_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGFL6 | ENST00000361306.6 | c.490C>T | p.Arg164Cys | missense_variant | 5/12 | 1 | NM_015507.4 | A2 | |
EGFL6 | ENST00000380602.3 | c.490C>T | p.Arg164Cys | missense_variant | 5/12 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0149 AC: 1676AN: 112174Hom.: 33 Cov.: 23 AF XY: 0.0126 AC XY: 434AN XY: 34348
GnomAD3 exomes AF: 0.00432 AC: 778AN: 179967Hom.: 16 AF XY: 0.00277 AC XY: 179AN XY: 64545
GnomAD4 exome AF: 0.00146 AC: 1605AN: 1096314Hom.: 33 Cov.: 30 AF XY: 0.00108 AC XY: 391AN XY: 361780
GnomAD4 genome AF: 0.0150 AC: 1680AN: 112229Hom.: 33 Cov.: 23 AF XY: 0.0127 AC XY: 437AN XY: 34413
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at