16-30700869-A-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_006662.3(SRCAP):āc.45A>Gā(p.Leu15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,614,072 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 Likely benign (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 32)
Exomes š: 0.0000041 ( 0 hom. )
Consequence
SRCAP
NM_006662.3 synonymous
NM_006662.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.205
Genes affected
SRCAP (HGNC:16974): (Snf2 related CREBBP activator protein) This gene encodes the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex. The encoded protein is an ATPase that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. It can function as a transcriptional activator in Notch-mediated, CREB-mediated and steroid receptor-mediated transcription. Mutations in this gene cause Floating-Harbor syndrome, a rare disorder characterized by short stature, language deficits and dysmorphic facial features. [provided by RefSeq, Feb 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 16-30700869-A-G is Benign according to our data. Variant chr16-30700869-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2181137.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.205 with no splicing effect.
BS2
High AC in GnomAdExome4 at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRCAP | NM_006662.3 | c.45A>G | p.Leu15= | synonymous_variant | 3/34 | ENST00000262518.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRCAP | ENST00000262518.9 | c.45A>G | p.Leu15= | synonymous_variant | 3/34 | 2 | NM_006662.3 | P1 | |
SRCAP | ENST00000411466.7 | c.45A>G | p.Leu15= | synonymous_variant | 3/34 | 3 | P1 | ||
SRCAP | ENST00000706321.1 | c.45A>G | p.Leu15= | synonymous_variant | 3/34 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248838Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135048
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GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461832Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727222
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74382
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 23, 2022 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at