12-110436687-G-GAAAAA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001278556.2(ARPC3):c.253-9_253-5dupTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00227 in 803,946 control chromosomes in the GnomAD database, including 19 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 13 hom., cov: 0)
Exomes 𝑓: 0.00093 ( 6 hom. )
Consequence
ARPC3
NM_001278556.2 splice_region, intron
NM_001278556.2 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.29
Genes affected
ARPC3 (HGNC:706): (actin related protein 2/3 complex subunit 3) This gene encodes one of seven subunits of the human Arp2/3 protein complex. The Arp2/3 protein complex has been conserved through evolution and is implicated in the control of actin polymerization in cells. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 12-110436687-G-GAAAAA is Benign according to our data. Variant chr12-110436687-G-GAAAAA is described in ClinVar as [Benign]. Clinvar id is 785427.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0136 (1157/85374) while in subpopulation AFR AF= 0.0177 (435/24598). AF 95% confidence interval is 0.0163. There are 13 homozygotes in gnomad4. There are 503 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARPC3 | NM_001278556.2 | c.253-9_253-5dupTTTTT | splice_region_variant, intron_variant | Intron 4 of 6 | ENST00000228825.12 | NP_001265485.1 | ||
ARPC3 | NM_001287222.2 | c.253-9_253-5dupTTTTT | splice_region_variant, intron_variant | Intron 4 of 6 | NP_001274151.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0136 AC: 1159AN: 85346Hom.: 13 Cov.: 0
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GnomAD3 exomes AF: 0.000617 AC: 81AN: 131236Hom.: 0 AF XY: 0.000445 AC XY: 32AN XY: 71968
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GnomAD4 exome AF: 0.000931 AC: 669AN: 718572Hom.: 6 Cov.: 24 AF XY: 0.00102 AC XY: 379AN XY: 373242
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GnomAD4 genome AF: 0.0136 AC: 1157AN: 85374Hom.: 13 Cov.: 0 AF XY: 0.0126 AC XY: 503AN XY: 39878
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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
Jun 16, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at