7-64991268-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001007253.4(ERV3-1):āc.1759A>Gā(p.Ile587Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000407 in 741,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001007253.4 missense
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 |
---|---|---|---|---|---|---|---|
ERV3-1 | NM_001007253.4 | c.1759A>G | p.Ile587Val | missense_variant | 2/2 | ENST00000394323.3 | |
ERV3-1-ZNF117 | NM_001348050.2 | c.-195-9152A>G | intron_variant | ||||
ERV3-1 | NM_001396062.1 | c.1759A>G | p.Ile587Val | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERV3-1 | ENST00000394323.3 | c.1759A>G | p.Ile587Val | missense_variant | 2/2 | 2 | NM_001007253.4 | P1 | |
ZNF117 | ENST00000487644.1 | n.145-9152A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000329 AC: 63AN: 191462Hom.: 0 AF XY: 0.000281 AC XY: 29AN XY: 103162
GnomAD4 exome AF: 0.000424 AC: 250AN: 589000Hom.: 0 Cov.: 0 AF XY: 0.000362 AC XY: 116AN XY: 320264
GnomAD4 genome AF: 0.000341 AC: 52AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.000268 AC XY: 20AN XY: 74500
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 01, 2022 | The c.1759A>G (p.I587V) alteration is located in exon 2 (coding exon 1) of the ERV3-1 gene. This alteration results from a A to G substitution at nucleotide position 1759, causing the isoleucine (I) at amino acid position 587 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