7-99035506-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_181349.3(SMURF1):c.2011+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,614,020 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0060 ( 13 hom., cov: 33)
Exomes 𝑓: 0.00084 ( 9 hom. )
Consequence
SMURF1
NM_181349.3 intron
NM_181349.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.322
Genes affected
SMURF1 (HGNC:16807): (SMAD specific E3 ubiquitin protein ligase 1) This gene encodes a ubiquitin ligase that is specific for receptor-regulated SMAD proteins in the bone morphogenetic protein (BMP) pathway. This protein plays a key roll in the regulation of cell motility, cell signalling, and cell polarity. Alternative splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Dec 2010]
TRRAP (HGNC:12347): (transformation/transcription domain associated protein) This gene encodes a large multidomain protein of the phosphoinositide 3-kinase-related kinases (PIKK) family. The encoded protein is a common component of many histone acetyltransferase (HAT) complexes and plays a role in transcription and DNA repair by recruiting HAT complexes to chromatin. Deregulation of this gene may play a role in several types of cancer including glioblastoma multiforme. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 7-99035506-G-A is Benign according to our data. Variant chr7-99035506-G-A is described in ClinVar as [Benign]. Clinvar id is 712665.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00595 (907/152324) while in subpopulation AFR AF= 0.0201 (837/41574). AF 95% confidence interval is 0.019. There are 13 homozygotes in gnomad4. There are 434 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 903 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMURF1 | NM_181349.3 | c.2011+9C>T | intron_variant | ENST00000361368.7 | |||
LOC101927550 | NR_110102.1 | n.2427G>A | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMURF1 | ENST00000361368.7 | c.2011+9C>T | intron_variant | 1 | NM_181349.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00593 AC: 903AN: 152206Hom.: 13 Cov.: 33
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GnomAD3 exomes AF: 0.00184 AC: 462AN: 251148Hom.: 6 AF XY: 0.00149 AC XY: 202AN XY: 135796
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GnomAD4 exome AF: 0.000845 AC: 1235AN: 1461696Hom.: 9 Cov.: 30 AF XY: 0.000792 AC XY: 576AN XY: 727140
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 20, 2018 | - - |
Computational 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at