6-11105258-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_207582.3(ERVFRD-1):c.53G>A(p.Arg18His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_207582.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERVFRD-1 | ENST00000472091.2 | c.53G>A | p.Arg18His | missense_variant | Exon 2 of 2 | 1 | NM_207582.3 | ENSP00000420174.1 | ||
SMIM13 | ENST00000416247.4 | c.76+10869C>T | intron_variant | Intron 1 of 1 | 1 | NM_001135575.2 | ENSP00000451866.1 | |||
ERVFRD-1 | ENST00000542862.1 | c.53G>A | p.Arg18His | missense_variant | Exon 1 of 1 | 6 | ||||
SMIM13 | ENST00000376935.4 | n.76+10869C>T | intron_variant | Intron 1 of 2 | 5 | ENSP00000452219.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251030Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135664
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461840Hom.: 0 Cov.: 32 AF XY: 0.0000468 AC XY: 34AN XY: 727218
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.53G>A (p.R18H) alteration is located in exon 2 (coding exon 1) of the ERVFRD-1 gene. This alteration results from a G to A substitution at nucleotide position 53, causing the arginine (R) at amino acid position 18 to be replaced by a histidine (H). 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