4-5685479-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_147127.5(EVC2):āc.707T>Cā(p.Val236Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 18/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_147127.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVC2 | NM_147127.5 | c.707T>C | p.Val236Ala | missense_variant, splice_region_variant | 6/22 | ENST00000344408.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVC2 | ENST00000344408.10 | c.707T>C | p.Val236Ala | missense_variant, splice_region_variant | 6/22 | 1 | NM_147127.5 | P2 | |
EVC2 | ENST00000310917.6 | c.467T>C | p.Val156Ala | missense_variant, splice_region_variant | 6/22 | 1 | A2 | ||
EVC2 | ENST00000475313.5 | c.467T>C | p.Val156Ala | missense_variant, splice_region_variant, NMD_transcript_variant | 6/23 | 1 | |||
EVC2 | ENST00000509670.1 | c.467T>C | p.Val156Ala | missense_variant, splice_region_variant, NMD_transcript_variant | 7/23 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251254Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135814
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461684Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727156
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
Ellis-van Creveld syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Feb 22, 2017 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | EVC2: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at