chr1-29148602-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM1BP4_StrongBS2
The NM_005626.5(SRSF4):c.1293T>A(p.Ser431Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000651 in 1,613,324 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_005626.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRSF4 | NM_005626.5 | c.1293T>A | p.Ser431Arg | missense_variant | 6/6 | ENST00000373795.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRSF4 | ENST00000373795.7 | c.1293T>A | p.Ser431Arg | missense_variant | 6/6 | 1 | NM_005626.5 | P1 | |
SRSF4 | ENST00000634348.1 | n.7379T>A | non_coding_transcript_exon_variant | 7/7 | 5 | ||||
SRSF4 | ENST00000691479.1 | c.*1500T>A | 3_prime_UTR_variant, NMD_transcript_variant | 10/10 |
Frequencies
GnomAD3 genomes AF: 0.0000660 AC: 10AN: 151552Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251374Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135858
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461772Hom.: 0 Cov.: 29 AF XY: 0.0000564 AC XY: 41AN XY: 727162
GnomAD4 genome AF: 0.0000660 AC: 10AN: 151552Hom.: 0 Cov.: 32 AF XY: 0.0000406 AC XY: 3AN XY: 73970
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.1293T>A (p.S431R) alteration is located in exon 6 (coding exon 6) of the SRSF4 gene. This alteration results from a T to A substitution at nucleotide position 1293, causing the serine (S) at amino acid position 431 to be replaced by an arginine (R). 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