rs10514350

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The XR_007058864.1(LOC107986434):​n.3087A>G variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,694 control chromosomes in the GnomAD database, including 2,795 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 0.18 ( 2795 hom., cov: 32)

Consequence

LOC107986434
XR_007058864.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.38
Variant links:
Genes affected
ARRDC3-AS1 (HGNC:44145): (ARRDC3 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.18).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC107986434XR_007058864.1 linkuse as main transcriptn.3087A>G non_coding_transcript_exon_variant 1/2
LOC107986434XR_001742804.2 linkuse as main transcriptn.3040+47A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARRDC3-AS1ENST00000701059.1 linkuse as main transcriptn.662-2905A>G intron_variant, non_coding_transcript_variant
ARRDC3-AS1ENST00000664205.1 linkuse as main transcriptn.190-2905A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.179
AC:
27114
AN:
151578
Hom.:
2794
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.100
Gnomad AMI
AF:
0.184
Gnomad AMR
AF:
0.144
Gnomad ASJ
AF:
0.182
Gnomad EAS
AF:
0.0482
Gnomad SAS
AF:
0.224
Gnomad FIN
AF:
0.251
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.230
Gnomad OTH
AF:
0.181
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.179
AC:
27118
AN:
151694
Hom.:
2795
Cov.:
32
AF XY:
0.180
AC XY:
13317
AN XY:
74108
show subpopulations
Gnomad4 AFR
AF:
0.100
Gnomad4 AMR
AF:
0.144
Gnomad4 ASJ
AF:
0.182
Gnomad4 EAS
AF:
0.0484
Gnomad4 SAS
AF:
0.224
Gnomad4 FIN
AF:
0.251
Gnomad4 NFE
AF:
0.230
Gnomad4 OTH
AF:
0.178
Alfa
AF:
0.211
Hom.:
453
Bravo
AF:
0.163
Asia WGS
AF:
0.121
AC:
422
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.18
CADD
Benign
21
DANN
Benign
0.87

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: rs10514350; hg19: chr5-90903609; API