rs764412749
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_006494.4(ERF):c.1636C>T(p.Arg546*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000334 in 1,498,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_006494.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERF | NM_006494.4 | c.1636C>T | p.Arg546* | stop_gained | Exon 4 of 4 | ENST00000222329.9 | NP_006485.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERF | ENST00000222329.9 | c.1636C>T | p.Arg546* | stop_gained | Exon 4 of 4 | 1 | NM_006494.4 | ENSP00000222329.3 | ||
ENSG00000268643 | ENST00000594664.1 | c.22+6502C>T | intron_variant | Intron 1 of 4 | 3 | ENSP00000470087.1 | ||||
ERF | ENST00000440177.6 | c.1411C>T | p.Arg471* | stop_gained | Exon 4 of 4 | 2 | ENSP00000388173.2 | |||
ENSG00000268643 | ENST00000676949.1 | n.30+114C>T | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151890Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000178 AC: 3AN: 168108Hom.: 0 AF XY: 0.0000112 AC XY: 1AN XY: 89666
GnomAD4 exome AF: 0.00000297 AC: 4AN: 1346442Hom.: 0 Cov.: 32 AF XY: 0.00000456 AC XY: 3AN XY: 657852
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151890Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74192
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1636C>T (p.R546*) alteration, located in exon 4 (coding exon 4) of the ERF gene, consists of a C to T substitution at nucleotide position 1636. This changes the amino acid from an arginine (R) to a stop codon at amino acid position 546. This alteration occurs at the 3' terminus of the ERF gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 3 amino acids (0.5%) of the protein. The exact functional effect of this alteration is unknown. Based on data from the Genome Aggregation Database (gnomAD) database, the ERF c.1636C>T alteration was observed in 0.0018% (3/168108) of total alleles studied. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Abdominal distention;C0018817:Atrial septal defect;C0018818:Ventricular septal defect;C0020295:Hydronephrosis;C0021843:Intestinal obstruction;C0236124:Gastrointestinal obstruction;C0265783:Pulmonary hypoplasia;C1145670:Respiratory failure;C2677180:Primary microcephaly;C4025279:Respiratory failure requiring assisted ventilation;C5441745:Abnormal pulmonary interstitial morphology Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at