rs13139128
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_003601.4(SMARCA5):āc.2424T>Cā(p.Asn808=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.999 in 1,609,866 control chromosomes in the GnomAD database, including 803,448 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 1.0 ( 75401 hom., cov: 30)
Exomes š: 1.0 ( 728047 hom. )
Consequence
SMARCA5
NM_003601.4 synonymous
NM_003601.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.589
Genes affected
SMARCA5 (HGNC:11101): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5) The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The protein encoded by this gene is a component of the chromatin remodeling and spacing factor RSF, a facilitator of the transcription of class II genes by RNA polymerase II. The encoded protein is similar in sequence to the Drosophila ISWI chromatin remodeling protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP7
?
Synonymous conserved (PhyloP=0.589 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCA5 | NM_003601.4 | c.2424T>C | p.Asn808= | synonymous_variant | 19/24 | ENST00000283131.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA5 | ENST00000283131.4 | c.2424T>C | p.Asn808= | synonymous_variant | 19/24 | 1 | NM_003601.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.995 AC: 151409AN: 152136Hom.: 75348 Cov.: 30
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GnomAD3 exomes AF: 0.999 AC: 248587AN: 248914Hom.: 124132 AF XY: 0.999 AC XY: 134521AN XY: 134666
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GnomAD4 exome AF: 0.999 AC: 1456849AN: 1457612Hom.: 728047 Cov.: 31 AF XY: 1.00 AC XY: 725032AN XY: 725388
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GnomAD4 genome ? AF: 0.995 AC: 151521AN: 152254Hom.: 75401 Cov.: 30 AF XY: 0.995 AC XY: 74077AN XY: 74438
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at