11-77667287-T-C
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_ModerateBS2
The NM_016578.4(RSF1):c.3956A>G(p.Asn1319Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict 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
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RSF1 | NM_016578.4 | c.3956A>G | p.Asn1319Ser | missense_variant | Exon 16 of 16 | ENST00000308488.11 | NP_057662.3 | |
RSF1 | XM_005274051.3 | c.3947A>G | p.Asn1316Ser | missense_variant | Exon 16 of 16 | XP_005274108.1 | ||
RSF1 | XM_017017923.2 | c.3833A>G | p.Asn1278Ser | 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.3956A>G | p.Asn1319Ser | missense_variant | Exon 16 of 16 | 1 | NM_016578.4 | ENSP00000311513.6 | ||
RSF1 | ENST00000480887.5 | c.3200A>G | p.Asn1067Ser | missense_variant | Exon 11 of 11 | 1 | ENSP00000434509.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461872Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727240 show subpopulations
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3956A>G (p.N1319S) alteration is located in exon 16 (coding exon 16) of the RSF1 gene. This alteration results from a A to G substitution at nucleotide position 3956, causing the asparagine (N) at amino acid position 1319 to be replaced by a serine (S). 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