chr19-7647307-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006949.4(STXBP2):c.1539-47G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,611,754 control chromosomes in the GnomAD database, including 45,881 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.1539-47G>A | intron_variant | Intron 17 of 18 | 1 | NM_006949.4 | ENSP00000221283.4 | |||
ENSG00000268400 | ENST00000698368.1 | n.*1642-47G>A | intron_variant | Intron 19 of 19 | ENSP00000513686.1 |
Frequencies
GnomAD3 genomes AF: 0.214 AC: 32481AN: 152084Hom.: 3594 Cov.: 33
GnomAD3 exomes AF: 0.208 AC: 49872AN: 239806Hom.: 5417 AF XY: 0.207 AC XY: 27201AN XY: 131434
GnomAD4 exome AF: 0.238 AC: 346814AN: 1459552Hom.: 42282 Cov.: 56 AF XY: 0.235 AC XY: 170723AN XY: 726110
GnomAD4 genome AF: 0.214 AC: 32501AN: 152202Hom.: 3599 Cov.: 33 AF XY: 0.210 AC XY: 15654AN XY: 74410
ClinVar
Submissions by phenotype
not specified Benign:2
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This variant is classified as Benign based on local population frequency. This variant was detected in 41% of patients studied by a panel of primary immunodeficiencies. Number of patients: 39. Only high quality variants are reported. -
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at