chr7-27245957-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001989.5(EVX1):c.756C>A(p.Asp252Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000222 in 1,609,240 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001989.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EVX1 | NM_001989.5 | c.756C>A | p.Asp252Glu | missense_variant | Exon 3 of 3 | ENST00000496902.7 | NP_001980.1 | |
EVX1 | NM_001304519.2 | c.210C>A | p.Asp70Glu | missense_variant | Exon 3 of 3 | NP_001291448.1 | ||
EVX1 | NM_001304520.2 | c.210C>A | p.Asp70Glu | missense_variant | Exon 4 of 4 | NP_001291449.1 | ||
EVX1-AS | NR_120507.1 | n.269+1004G>T | intron_variant | Intron 1 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EVX1 | ENST00000496902.7 | c.756C>A | p.Asp252Glu | missense_variant | Exon 3 of 3 | 1 | NM_001989.5 | ENSP00000419266.3 | ||
EVX1 | ENST00000222761.7 | c.*95C>A | 3_prime_UTR_variant | Exon 3 of 3 | 1 | ENSP00000222761.3 | ||||
EVX1 | ENST00000580535.1 | c.*95C>A | 3_prime_UTR_variant | Exon 4 of 4 | 2 | ENSP00000463759.1 | ||||
EVX1-AS | ENST00000517726.1 | n.269+1004G>T | intron_variant | Intron 1 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000252 AC: 61AN: 242268Hom.: 0 AF XY: 0.000279 AC XY: 37AN XY: 132586
GnomAD4 exome AF: 0.000205 AC: 299AN: 1456916Hom.: 0 Cov.: 31 AF XY: 0.000232 AC XY: 168AN XY: 725068
GnomAD4 genome AF: 0.000381 AC: 58AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.756C>A (p.D252E) alteration is located in exon 3 (coding exon 3) of the EVX1 gene. This alteration results from a C to A substitution at nucleotide position 756, causing the aspartic acid (D) at amino acid position 252 to be replaced by a glutamic acid (E). 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