Genetic Variant ARPC3:c.253-9_253-5dupTTTTT (chr12-110436687-G-GAAAAA) – ACMG Classification: Benign (-10 pts)

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.29

Variant links:

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]

ARPC3 links:

ENSG00000258210 (HGNC:):

ENSG00000258210 links:

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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 link	c.253-9_253-5dupTTTTT		splice_region_variant, intron_variant	Intron 4 of 6	ENST00000228825.12	NP_001265485.1	O15145
ARPC3	NM_001287222.2 link	c.253-9_253-5dupTTTTT		splice_region_variant, intron_variant	Intron 4 of 6		NP_001274151.1	O15145

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARPC3	ENST00000228825.12 link	c.253-5_253-4insTTTTT		splice_region_variant, intron_variant	Intron 4 of 6	1	NM_001278556.2	ENSP00000228825.7		O15145

Frequencies

GnomAD3 genomes

AF:

0.0136

AC:

1159

AN:

85346

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0178

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.00689

Gnomad ASJ

AF:

0.0145

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0137

Gnomad FIN

AF:

0.000290

Gnomad MID

AF:

0.00990

Gnomad NFE

AF:

0.0139

Gnomad OTH

AF:

0.0224

GnomAD3 exomes

AF:

0.000617

AC:

AN:

131236

Hom.:

AF XY:

0.000445

AC XY:

AN XY:

71968

show subpopulations

Gnomad AFR exome

AF:

0.00496

Gnomad AMR exome

AF:

0.000362

Gnomad ASJ exome

AF:

0.00111

Gnomad EAS exome

AF:

0.0000974

Gnomad SAS exome

AF:

0.000354

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000493

Gnomad OTH exome

AF:

0.000596

GnomAD4 exome

AF:

0.000931

AC:

669

AN:

718572

Hom.:

Cov.:

AF XY:

0.00102

AC XY:

379

AN XY:

373242

show subpopulations

Gnomad4 AFR exome

AF:

0.00542

Gnomad4 AMR exome

AF:

0.000715

Gnomad4 ASJ exome

AF:

0.00184

Gnomad4 EAS exome

AF:

0.0000411

Gnomad4 SAS exome

AF:

0.000840

Gnomad4 FIN exome

AF:

0.000154

Gnomad4 NFE exome

AF:

0.000888

Gnomad4 OTH exome

AF:

0.00128

GnomAD4 genome

AF:

0.0136

AC:

1157

AN:

85374

Hom.:

Cov.:

AF XY:

0.0126

AC XY:

503

AN XY:

39878

show subpopulations

Gnomad4 AFR

AF:

0.0177

Gnomad4 AMR

AF:

0.00688

Gnomad4 ASJ

AF:

0.0145

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0138

Gnomad4 FIN

AF:

0.000290

Gnomad4 NFE

AF:

0.0139

Gnomad4 OTH

AF:

0.0223

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over