20-43458050-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_006275.6(SRSF6):c.17T>C(p.Ile6Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,612,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006275.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRSF6 | NM_006275.6 | c.17T>C | p.Ile6Thr | missense_variant | Exon 1 of 6 | ENST00000244020.5 | NP_006266.2 | |
SRSF6 | XM_047440372.1 | c.17T>C | p.Ile6Thr | missense_variant | Exon 1 of 3 | XP_047296328.1 | ||
SRSF6 | NR_034009.2 | n.155T>C | non_coding_transcript_exon_variant | Exon 1 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRSF6 | ENST00000244020.5 | c.17T>C | p.Ile6Thr | missense_variant | Exon 1 of 6 | 1 | NM_006275.6 | ENSP00000244020.3 | ||
ENSG00000288000 | ENST00000657241.1 | c.-5T>C | upstream_gene_variant | ENSP00000499734.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249430Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135242
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460664Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726626
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.17T>C (p.I6T) alteration is located in exon 1 (coding exon 1) of the SRSF6 gene. This alteration results from a T to C substitution at nucleotide position 17, causing the isoleucine (I) at amino acid position 6 to be replaced by a threonine (T). 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