11-77667353-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_016578.4(RSF1):c.3890G>A(p.Arg1297His) variant causes a missense change. The variant allele was found at a frequency of 0.0000229 in 1,613,838 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016578.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RSF1 | NM_016578.4 | c.3890G>A | p.Arg1297His | missense_variant | Exon 16 of 16 | ENST00000308488.11 | NP_057662.3 | |
RSF1 | XM_005274051.3 | c.3881G>A | p.Arg1294His | missense_variant | Exon 16 of 16 | XP_005274108.1 | ||
RSF1 | XM_017017923.2 | c.3767G>A | p.Arg1256His | missense_variant | Exon 16 of 16 | XP_016873412.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RSF1 | ENST00000308488.11 | c.3890G>A | p.Arg1297His | missense_variant | Exon 16 of 16 | 1 | NM_016578.4 | ENSP00000311513.6 | ||
RSF1 | ENST00000480887.5 | c.3134G>A | p.Arg1045His | missense_variant | Exon 11 of 11 | 1 | ENSP00000434509.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251218Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135772
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461694Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727158
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3890G>A (p.R1297H) alteration is located in exon 16 (coding exon 16) of the RSF1 gene. This alteration results from a G to A substitution at nucleotide position 3890, causing the arginine (R) at amino acid position 1297 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