19-7645324-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006949.4(STXBP2):c.1356+18A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 1,563,216 control chromosomes in the GnomAD database, including 124,415 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006949.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STXBP2 | ENST00000221283.10 | c.1356+18A>G | intron_variant | Intron 15 of 18 | 1 | NM_006949.4 | ENSP00000221283.4 | |||
ENSG00000268400 | ENST00000698368.1 | n.*1459+18A>G | intron_variant | Intron 17 of 19 | ENSP00000513686.1 |
Frequencies
GnomAD3 genomes AF: 0.445 AC: 67619AN: 152006Hom.: 15704 Cov.: 34
GnomAD3 exomes AF: 0.423 AC: 74270AN: 175436Hom.: 16419 AF XY: 0.415 AC XY: 38790AN XY: 93478
GnomAD4 exome AF: 0.386 AC: 544019AN: 1411092Hom.: 108677 Cov.: 32 AF XY: 0.384 AC XY: 267644AN XY: 697502
GnomAD4 genome AF: 0.445 AC: 67710AN: 152124Hom.: 15738 Cov.: 34 AF XY: 0.451 AC XY: 33564AN XY: 74362
ClinVar
Submissions by phenotype
not specified Benign:3
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This variant is classified as Benign based on local population frequency. This variant was detected in 70% of patients studied by a panel of primary immunodeficiencies. Number of patients: 67. Only high quality variants are reported. -
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Familial hemophagocytic lymphohistiocytosis 5 Benign:2
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at