11-77667369-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_016578.4(RSF1):c.3874G>A(p.Glu1292Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000242 in 1,613,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RSF1 | NM_016578.4 | c.3874G>A | p.Glu1292Lys | missense_variant | Exon 16 of 16 | ENST00000308488.11 | NP_057662.3 | |
RSF1 | XM_005274051.3 | c.3865G>A | p.Glu1289Lys | missense_variant | Exon 16 of 16 | XP_005274108.1 | ||
RSF1 | XM_017017923.2 | c.3751G>A | p.Glu1251Lys | 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.3874G>A | p.Glu1292Lys | missense_variant | Exon 16 of 16 | 1 | NM_016578.4 | ENSP00000311513.6 | ||
RSF1 | ENST00000480887.5 | c.3118G>A | p.Glu1040Lys | missense_variant | Exon 11 of 11 | 1 | ENSP00000434509.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251248Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135786
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461600Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 727122
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3874G>A (p.E1292K) 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 3874, causing the glutamic acid (E) at amino acid position 1292 to be replaced by a lysine (K). 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