rs1650937
Positions:
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
ENST00000597698.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.58
Genes affected
ARPC1AP2 (HGNC:56495): (ARPC1A pseudogene 2)
Genome browser will be placed here
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 | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARPC1AP2 | ENST00000597698.1 | n.922C>A | non_coding_transcript_exon_variant | 1/1 | |||||
ZNF702P | ENST00000600425.5 | n.130-18115G>T | intron_variant, non_coding_transcript_variant | 3 | |||||
ZNF702P | ENST00000594516.1 | n.160-18115G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.254 AC: 38699AN: 152068Hom.: 9111 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
38699
AN:
152068
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.109 AC: 139956AN: 1282306Hom.: 14461 Cov.: 24 AF XY: 0.107 AC XY: 69008AN XY: 646324
GnomAD4 exome
AF:
AC:
139956
AN:
1282306
Hom.:
Cov.:
24
AF XY:
AC XY:
69008
AN XY:
646324
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.255 AC: 38765AN: 152188Hom.: 9128 Cov.: 32 AF XY: 0.253 AC XY: 18823AN XY: 74400
GnomAD4 genome
?
AF:
AC:
38765
AN:
152188
Hom.:
Cov.:
32
AF XY:
AC XY:
18823
AN XY:
74400
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
890
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at