chr6-89098885-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080743.5(SRSF12):c.479G>A(p.Arg160Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080743.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRSF12 | ENST00000452027.3 | c.479G>A | p.Arg160Gln | missense_variant | Exon 5 of 5 | 1 | NM_080743.5 | ENSP00000414302.2 | ||
SRSF12 | ENST00000524221.1 | n.761G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
SRSF12 | ENST00000488604.1 | n.*52G>A | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151964Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249166Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135166
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461682Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 727126
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151964Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74206
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.479G>A (p.R160Q) alteration is located in exon 5 (coding exon 5) of the SRSF12 gene. This alteration results from a G to A substitution at nucleotide position 479, causing the arginine (R) at amino acid position 160 to be replaced by a glutamine (Q). 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