rs13403276

Variant names:

• chr2-218216574-T-C
• rs13403276
• ENST00000811911.1:n.391A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000811911.1(ENSG00000305602):​n.391A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 152,264 control chromosomes in the GnomAD database, including 177 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.040 (177 hom., cov: 32)
• Consequence: ENSG00000305602 ENST00000811911.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 12 publications found

Genes affected

ENSG00000305602 (HGNC:):

ARPC2 (HGNC:705): (actin related protein 2/3 complex subunit 2) This gene encodes one of seven subunits of the human Arp2/3 protein complex. The Arp2/3 protein complex has been implicated in the control of actin polymerization in cells and has been conserved through evolution. The exact role of the protein encoded by this gene, the p34 subunit, has yet to be determined. Two alternatively spliced variants have been characterized to date. Additional alternatively spliced variants have been described but their full length nature has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811911.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305602	ENST00000811911.1		n.391A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000305602	ENST00000811912.1		n.368A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000305602	ENST00000811914.1		n.378A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6082 AN: 152146 Hom.: 177 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0634

Gnomad OTH AF: 0.0459

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0399 AC: 6077 AN: 152264 Hom.: 177 Cov.: 32 AF XY: 0.0375 AC XY: 2789 AN XY: 74468

African (AFR) AF: 0.0105 AC: 436 AN: 41552

American (AMR) AF: 0.0388 AC: 594 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0430 AC: 149 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4826

European-Finnish (FIN) AF: 0.0374 AC: 397 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0634 AC: 4309 AN: 68010

Other (OTH) AF: 0.0455 AC: 96 AN: 2112

Alfa AF: 0.0556 Hom.: 456

Bravo AF: 0.0388

Asia WGS AF: 0.00664 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	9.4
DANN	Benign	0.58
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs13403276; hg19: chr2-219081297;