11-30222321-G-T

Variant summary

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

The NR_187431.1(ARL14EP-DT):​n.250+94569C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,986 control chromosomes in the GnomAD database, including 38,383 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 0.71 ( 38383 hom., cov: 32)

Consequence

ARL14EP-DT
NR_187431.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.293
Variant links:
Genes affected

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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ARL14EP-DTNR_187431.1 linkuse as main transcriptn.250+94569C>A intron_variant
ARL14EP-DTNR_187432.1 linkuse as main transcriptn.429+94569C>A intron_variant
ARL14EP-DTNR_187433.1 linkuse as main transcriptn.250+94569C>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ARL14EP-DTENST00000662729.1 linkuse as main transcriptn.293-65468C>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.707
AC:
107353
AN:
151870
Hom.:
38350
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.802
Gnomad AMI
AF:
0.646
Gnomad AMR
AF:
0.684
Gnomad ASJ
AF:
0.623
Gnomad EAS
AF:
0.905
Gnomad SAS
AF:
0.691
Gnomad FIN
AF:
0.686
Gnomad MID
AF:
0.687
Gnomad NFE
AF:
0.649
Gnomad OTH
AF:
0.693
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.707
AC:
107431
AN:
151986
Hom.:
38383
Cov.:
32
AF XY:
0.711
AC XY:
52836
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.802
Gnomad4 AMR
AF:
0.684
Gnomad4 ASJ
AF:
0.623
Gnomad4 EAS
AF:
0.905
Gnomad4 SAS
AF:
0.690
Gnomad4 FIN
AF:
0.686
Gnomad4 NFE
AF:
0.649
Gnomad4 OTH
AF:
0.690
Alfa
AF:
0.662
Hom.:
67708
Bravo
AF:
0.710
Asia WGS
AF:
0.778
AC:
2705
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.97
DANN
Benign
0.36

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: rs1782507; hg19: chr11-30243868; API