chr4-52743945-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001242690.2(ERVMER34-1):āc.1576C>Gā(p.Leu526Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000624 in 1,121,352 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001242690.2 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 |
---|---|---|---|---|---|---|---|
ERVMER34-1 | NM_001242690.2 | c.1576C>G | p.Leu526Val | missense_variant | 3/3 | ENST00000443173.6 | |
ERVMER34-1 | NM_024534.6 | c.1576C>G | p.Leu526Val | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERVMER34-1 | ENST00000443173.6 | c.1576C>G | p.Leu526Val | missense_variant | 3/3 | 3 | NM_001242690.2 | P1 | |
ERVMER34-1 | ENST00000440542.1 | c.1576C>G | p.Leu526Val | missense_variant | 4/4 | 1 | P1 | ||
ERVMER34-1 | ENST00000454756.6 | n.384+6985C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000212 AC: 3AN: 141386Hom.: 0 AF XY: 0.0000133 AC XY: 1AN XY: 75298
GnomAD4 exome AF: 0.0000578 AC: 56AN: 969156Hom.: 0 Cov.: 13 AF XY: 0.0000404 AC XY: 20AN XY: 495346
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1576C>G (p.L526V) alteration is located in exon 4 (coding exon 1) of the ERVMER34-1 gene. This alteration results from a C to G substitution at nucleotide position 1576, causing the leucine (L) at amino acid position 526 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