Variant rs1650937 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000597698.1(ARPC1AP2):n.922C>A 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 0.125 in 1,434,494 control chromosomes in the GnomAD database, including 23,589 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 0.25 ( 9128 hom., cov: 32)

Exomes 𝑓: 0.11 ( 14461 hom. )

Consequence

ARPC1AP2
ENST00000597698.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.58

Variant links:

Genes affected

ARPC1AP2 (HGNC:56495): (ARPC1A pseudogene 2)

ARPC1AP2 links:

ZNF702P (HGNC:25775): (zinc finger protein 702, pseudogene) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF702P links:

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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=-0.65).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ARPC1AP2	ENST00000597698.1 linkuse as main transcript	n.922C>A	non_coding_transcript_exon_variant	1/1
ZNF702P	ENST00000600425.5 linkuse as main transcript	n.130-18115G>T	intron_variant, non_coding_transcript_variant		3
ZNF702P	ENST00000594516.1 linkuse as main transcript	n.160-18115G>T	intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38699

AN:

152068

Hom.:

9111

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.428

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.0700

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0825

Gnomad OTH

AF:

0.226

GnomAD4 exome

AF:

0.109

AC:

139956

AN:

1282306

Hom.:

14461

Cov.:

AF XY:

0.107

AC XY:

69008

AN XY:

646324

show subpopulations

Gnomad4 AFR exome

AF:

0.631

Gnomad4 AMR exome

AF:

0.192

Gnomad4 ASJ exome

AF:

0.115

Gnomad4 EAS exome

AF:

0.395

Gnomad4 SAS exome

AF:

0.104

Gnomad4 FIN exome

AF:

0.0739

Gnomad4 NFE exome

AF:

0.0778

Gnomad4 OTH exome

AF:

0.136

GnomAD4 genome

AF:

0.255

AC:

38765

AN:

152188

Hom.:

9128

Cov.:

AF XY:

0.253

AC XY:

18823

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.613

Gnomad4 AMR

AF:

0.209

Gnomad4 ASJ

AF:

0.115

Gnomad4 EAS

AF:

0.427

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.0700

Gnomad4 NFE

AF:

0.0825

Gnomad4 OTH

AF:

0.226

Alfa

AF:

0.0564

Hom.:

Bravo

AF:

0.281

Asia WGS

AF:

0.255

AC:

890

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

1.2

DANN

Benign

0.55

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over