chr6-13286236-G-GT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_030948.6(PHACTR1):c.1727+24dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0111 in 1,370,204 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 1 hom., cov: 32)
Exomes 𝑓: 0.012 ( 1 hom. )
Consequence
PHACTR1
NM_030948.6 intron
NM_030948.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.588
Genes affected
PHACTR1 (HGNC:20990): (phosphatase and actin regulator 1) The protein encoded by this gene is a member of the phosphatase and actin regulator family of proteins. This family member can bind actin and regulate the reorganization of the actin cytoskeleton. It plays a role in tubule formation and in endothelial cell survival. Polymorphisms in this gene are associated with susceptibility to myocardial infarction, coronary artery disease and cervical artery dissection. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2016]
TBC1D7 (HGNC:21066): (TBC1 domain family member 7) This gene encodes a member of the TBC-domain containing protein family. The encoded protein functions as a subunit of the tuberous sclerosis TSC1-TSC2 complex which plays a role in the regulation of cellular growth and differentiation. Mutations in this gene have been associated with autosomal recessive megalencephaly. Alternative splicing results in multiple transcript variants. Naturally occurring readthrough transcription occurs between this locus and downstream LOC100130357. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 6-13286236-G-GT is Benign according to our data. Variant chr6-13286236-G-GT is described in ClinVar as [Likely_benign]. Clinvar id is 3024709.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0122 (14877/1221312) while in subpopulation AMR AF= 0.0168 (432/25712). AF 95% confidence interval is 0.0155. There are 1 homozygotes in gnomad4_exome. There are 7465 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
?
High AC in GnomAd at 279 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHACTR1 | NM_030948.6 | c.1727+24dup | intron_variant | ENST00000332995.12 | |||
TBC1D7-LOC100130357 | NR_134872.2 | n.713-4684_713-4683insA | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHACTR1 | ENST00000332995.12 | c.1727+24dup | intron_variant | 2 | NM_030948.6 | P3 | |||
ENST00000606150.5 | n.319-4684_319-4683insA | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00188 AC: 279AN: 148780Hom.: 1 Cov.: 32
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GnomAD4 exome AF: 0.0122 AC: 14877AN: 1221312Hom.: 1 Cov.: 29 AF XY: 0.0124 AC XY: 7465AN XY: 602202
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GnomAD4 genome ? AF: 0.00187 AC: 278AN: 148892Hom.: 1 Cov.: 32 AF XY: 0.00180 AC XY: 131AN XY: 72616
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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 | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | PHACTR1: BS1 - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at