chrX-13594844-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015507.4(EGFL6):c.196G>A(p.Glu66Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.003 in 1,207,051 control chromosomes in the GnomAD database, including 68 homozygotes. There are 942 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict 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.196G>A | p.Glu66Lys | missense_variant | 3/12 | ENST00000361306.6 | |
EGFL6 | NM_001167890.2 | c.196G>A | p.Glu66Lys | missense_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGFL6 | ENST00000361306.6 | c.196G>A | p.Glu66Lys | missense_variant | 3/12 | 1 | NM_015507.4 | A2 | |
EGFL6 | ENST00000380602.3 | c.196G>A | p.Glu66Lys | missense_variant | 3/12 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0155 AC: 1733AN: 111521Hom.: 33 Cov.: 23 AF XY: 0.0137 AC XY: 462AN XY: 33729
GnomAD3 exomes AF: 0.00465 AC: 848AN: 182351Hom.: 12 AF XY: 0.00326 AC XY: 218AN XY: 66873
GnomAD4 exome AF: 0.00171 AC: 1878AN: 1095476Hom.: 35 Cov.: 29 AF XY: 0.00132 AC XY: 475AN XY: 360998
GnomAD4 genome AF: 0.0156 AC: 1741AN: 111575Hom.: 33 Cov.: 23 AF XY: 0.0138 AC XY: 467AN XY: 33793
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