chr22-30338880-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_005877.6(SF3A1):c.1652A>G(p.Asn551Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000551 in 1,614,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005877.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SF3A1 | NM_005877.6 | c.1652A>G | p.Asn551Ser | missense_variant | 11/16 | ENST00000215793.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SF3A1 | ENST00000215793.13 | c.1652A>G | p.Asn551Ser | missense_variant | 11/16 | 1 | NM_005877.6 | P1 | |
SF3A1 | ENST00000444440.1 | c.605A>G | p.Asn202Ser | missense_variant | 4/5 | 5 | |||
SF3A1 | ENST00000485618.1 | n.553A>G | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
SF3A1 | ENST00000411423.1 | c.*151A>G | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000596 AC: 15AN: 251492Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135920
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461894Hom.: 0 Cov.: 32 AF XY: 0.0000509 AC XY: 37AN XY: 727248
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.1652A>G (p.N551S) alteration is located in exon 11 (coding exon 11) of the SF3A1 gene. This alteration results from a A to G substitution at nucleotide position 1652, causing the asparagine (N) at amino acid position 551 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