chr10-13333829-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_012247.5(SEPHS1):āc.548A>Gā(p.Asn183Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_012247.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEPHS1 | NM_012247.5 | c.548A>G | p.Asn183Ser | missense_variant | 5/9 | ENST00000327347.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPHS1 | ENST00000327347.10 | c.548A>G | p.Asn183Ser | missense_variant | 5/9 | 1 | NM_012247.5 | P1 | |
SEPHS1 | ENST00000545675.5 | c.347A>G | p.Asn116Ser | missense_variant | 4/8 | 1 | |||
SEPHS1 | ENST00000378614.8 | c.548A>G | p.Asn183Ser | missense_variant | 5/8 | 1 | |||
SEPHS1 | ENST00000413411.5 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250276Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135308
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460824Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726742
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.548A>G (p.N183S) alteration is located in exon 5 (coding exon 4) of the SEPHS1 gene. This alteration results from a A to G substitution at nucleotide position 548, causing the asparagine (N) at amino acid position 183 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