chr9-89325513-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024077.5(SECISBP2):c.269A>G(p.Tyr90Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000477 in 1,613,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024077.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SECISBP2 | NM_024077.5 | c.269A>G | p.Tyr90Cys | missense_variant | 3/17 | ENST00000375807.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SECISBP2 | ENST00000375807.8 | c.269A>G | p.Tyr90Cys | missense_variant | 3/17 | 1 | NM_024077.5 | P2 | |
SECISBP2 | ENST00000339901.8 | c.85-35A>G | intron_variant | 1 | A2 | ||||
SECISBP2 | ENST00000470305.1 | n.3314A>G | non_coding_transcript_exon_variant | 1/3 | 1 | ||||
SECISBP2 | ENST00000534113.6 | c.65A>G | p.Tyr22Cys | missense_variant | 3/17 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000552 AC: 84AN: 152044Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000807 AC: 203AN: 251432Hom.: 0 AF XY: 0.000832 AC XY: 113AN XY: 135884
GnomAD4 exome AF: 0.000469 AC: 686AN: 1461712Hom.: 0 Cov.: 31 AF XY: 0.000437 AC XY: 318AN XY: 727166
GnomAD4 genome ? AF: 0.000552 AC: 84AN: 152044Hom.: 0 Cov.: 33 AF XY: 0.000754 AC XY: 56AN XY: 74284
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2022 | The c.269A>G (p.Y90C) alteration is located in exon 3 (coding exon 3) of the SECISBP2 gene. This alteration results from a A to G substitution at nucleotide position 269, causing the tyrosine (Y) at amino acid position 90 to be replaced by a cysteine (C). 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