4-110488681-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001977.4(ENPEP):c.785C>T(p.Ala262Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 1,606,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 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 (★).
Frequency
Consequence
NM_001977.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENPEP | NM_001977.4 | c.785C>T | p.Ala262Val | missense_variant, splice_region_variant | 2/20 | ENST00000265162.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENPEP | ENST00000265162.10 | c.785C>T | p.Ala262Val | missense_variant, splice_region_variant | 2/20 | 1 | NM_001977.4 | P1 | |
ENPEP | ENST00000510961.1 | n.213C>T | splice_region_variant, non_coding_transcript_exon_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152040Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000165 AC: 4AN: 242782Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131220
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1454286Hom.: 0 Cov.: 33 AF XY: 0.0000111 AC XY: 8AN XY: 723324
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152040Hom.: 0 Cov.: 33 AF XY: 0.0000539 AC XY: 4AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2023 | The c.785C>T (p.A262V) alteration is located in exon 2 (coding exon 2) of the ENPEP gene. This alteration results from a C to T substitution at nucleotide position 785, causing the alanine (A) at amino acid position 262 to be replaced by a valine (V). 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