rs11755

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005717.4(ARPC5):​c.*531T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 153,550 control chromosomes in the GnomAD database, including 23,188 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 0.53 ( 23073 hom., cov: 32)
Exomes 𝑓: 0.41 ( 115 hom. )

Consequence

ARPC5
NM_005717.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260
Variant links:
Genes affected
ARPC5 (HGNC:708): (actin related protein 2/3 complex subunit 5) 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 p16 subunit, has yet to be determined. Alternatively spliced transcript variants encoding different isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

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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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARPC5NM_005717.4 linkuse as main transcriptc.*531T>C 3_prime_UTR_variant 4/4 ENST00000359856.11
ARPC5NM_001270439.2 linkuse as main transcriptc.*531T>C 3_prime_UTR_variant 4/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARPC5ENST00000359856.11 linkuse as main transcriptc.*531T>C 3_prime_UTR_variant 4/41 NM_005717.4 P3O15511-1
ARPC5ENST00000294742.6 linkuse as main transcriptc.*531T>C 3_prime_UTR_variant 4/41 A1O15511-2
ARPC5ENST00000367534.5 linkuse as main transcriptc.393+3460T>C intron_variant 3
ARPC5ENST00000462965.1 linkuse as main transcriptn.1648T>C non_coding_transcript_exon_variant 3/32

Frequencies

GnomAD3 genomes
AF:
0.531
AC:
80727
AN:
151964
Hom.:
23015
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.746
Gnomad AMI
AF:
0.409
Gnomad AMR
AF:
0.505
Gnomad ASJ
AF:
0.431
Gnomad EAS
AF:
0.245
Gnomad SAS
AF:
0.400
Gnomad FIN
AF:
0.459
Gnomad MID
AF:
0.494
Gnomad NFE
AF:
0.456
Gnomad OTH
AF:
0.509
GnomAD4 exome
AF:
0.413
AC:
606
AN:
1468
Hom.:
115
Cov.:
0
AF XY:
0.410
AC XY:
353
AN XY:
860
show subpopulations
Gnomad4 AMR exome
AF:
0.396
Gnomad4 ASJ exome
AF:
0.500
Gnomad4 EAS exome
AF:
0.100
Gnomad4 SAS exome
AF:
0.284
Gnomad4 FIN exome
AF:
0.450
Gnomad4 NFE exome
AF:
0.421
Gnomad4 OTH exome
AF:
0.413
GnomAD4 genome
AF:
0.532
AC:
80847
AN:
152082
Hom.:
23073
Cov.:
32
AF XY:
0.527
AC XY:
39173
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.747
Gnomad4 AMR
AF:
0.505
Gnomad4 ASJ
AF:
0.431
Gnomad4 EAS
AF:
0.245
Gnomad4 SAS
AF:
0.400
Gnomad4 FIN
AF:
0.459
Gnomad4 NFE
AF:
0.456
Gnomad4 OTH
AF:
0.514
Alfa
AF:
0.465
Hom.:
27891
Bravo
AF:
0.547
Asia WGS
AF:
0.372
AC:
1296
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
4.5
DANN
Benign
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs11755; hg19: chr1-183596136; API