chr9-89328784-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_024077.5(SECISBP2):c.699G>A(p.Met233Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000278 in 1,614,184 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_024077.5 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 |
---|---|---|---|---|---|---|---|
SECISBP2 | NM_024077.5 | c.699G>A | p.Met233Ile | missense_variant | 5/17 | ENST00000375807.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SECISBP2 | ENST00000375807.8 | c.699G>A | p.Met233Ile | missense_variant | 5/17 | 1 | NM_024077.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000861 AC: 131AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000266 AC: 67AN: 251462Hom.: 0 AF XY: 0.000235 AC XY: 32AN XY: 135906
GnomAD4 exome AF: 0.000215 AC: 315AN: 1461854Hom.: 2 Cov.: 31 AF XY: 0.000228 AC XY: 166AN XY: 727230
GnomAD4 genome ? AF: 0.000880 AC: 134AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.000846 AC XY: 63AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 30, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at