9-2029084-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_003070.5(SMARCA2):c.62C>A(p.Pro21His) variant causes a missense change. The variant allele was found at a frequency of 0.00000421 in 1,426,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003070.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMARCA2 | NM_003070.5 | c.62C>A | p.Pro21His | missense_variant | Exon 2 of 34 | ENST00000349721.8 | NP_003061.3 | |
SMARCA2 | NM_001289396.2 | c.62C>A | p.Pro21His | missense_variant | Exon 2 of 34 | NP_001276325.1 | ||
SMARCA2 | NM_139045.4 | c.62C>A | p.Pro21His | missense_variant | Exon 2 of 33 | NP_620614.2 | ||
SMARCA2 | NM_001289397.2 | c.62C>A | p.Pro21His | missense_variant | Exon 2 of 33 | NP_001276326.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000512 AC: 1AN: 195458Hom.: 0 AF XY: 0.00000949 AC XY: 1AN XY: 105372
GnomAD4 exome AF: 0.00000421 AC: 6AN: 1426524Hom.: 0 Cov.: 32 AF XY: 0.00000566 AC XY: 4AN XY: 706644
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.62C>A (p.P21H) alteration is located in exon 2 (coding exon 1) of the SMARCA2 gene. This alteration results from a C to A substitution at nucleotide position 62, causing the proline (P) at amino acid position 21 to be replaced by a histidine (H). 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