rs4533449

Variant summary

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

The XM_047446546.1(PPIAP60):​c.502-59T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 152,230 control chromosomes in the GnomAD database, including 37,590 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 0.70 ( 37547 hom., cov: 31)
Exomes 𝑓: 0.84 ( 43 hom. )

Consequence

PPIAP60
XM_047446546.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0130
Variant links:
Genes affected
LINC03037 (HGNC:56227): (long intergenic non-protein coding RNA 3037)

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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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PPIAP60XM_047446546.1 linkuse as main transcriptc.502-59T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC03037ENST00000430897.1 linkuse as main transcriptn.539+11A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.697
AC:
105968
AN:
151988
Hom.:
37495
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.605
Gnomad AMI
AF:
0.810
Gnomad AMR
AF:
0.745
Gnomad ASJ
AF:
0.601
Gnomad EAS
AF:
0.662
Gnomad SAS
AF:
0.604
Gnomad FIN
AF:
0.832
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.736
Gnomad OTH
AF:
0.653
GnomAD4 exome
AF:
0.844
AC:
103
AN:
122
Hom.:
43
Cov.:
0
AF XY:
0.829
AC XY:
58
AN XY:
70
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
1.00
Gnomad4 SAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.878
Gnomad4 NFE exome
AF:
0.727
Gnomad4 OTH exome
AF:
1.00
GnomAD4 genome
AF:
0.697
AC:
106073
AN:
152108
Hom.:
37547
Cov.:
31
AF XY:
0.700
AC XY:
52054
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.605
Gnomad4 AMR
AF:
0.745
Gnomad4 ASJ
AF:
0.601
Gnomad4 EAS
AF:
0.663
Gnomad4 SAS
AF:
0.606
Gnomad4 FIN
AF:
0.832
Gnomad4 NFE
AF:
0.736
Gnomad4 OTH
AF:
0.650
Alfa
AF:
0.719
Hom.:
78830
Bravo
AF:
0.686
Asia WGS
AF:
0.624
AC:
2172
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.5
DANN
Benign
0.47
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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.

Other links and lift over

dbSNP: rs4533449; hg19: chr2-11505213; API