rs11031006

Variant summary

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

The ENST00000662729.1(ARL14EP-DT):​n.293-48128C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,116 control chromosomes in the GnomAD database, including 1,022 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 0.11 ( 1022 hom., cov: 32)

Consequence

ARL14EP-DT
ENST00000662729.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.09
Variant links:
Genes affected
ARL14EP-DT (HGNC:55517): (ARL14EP divergent transcript)

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=-0.12).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARL14EP-DTXR_007062639.1 linkuse as main transcriptn.351+111909C>T intron_variant, non_coding_transcript_variant
ARL14EP-DTXR_931152.3 linkuse as main transcriptn.530+111909C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARL14EP-DTENST00000662729.1 linkuse as main transcriptn.293-48128C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.109
AC:
16619
AN:
151998
Hom.:
1019
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0592
Gnomad AMI
AF:
0.0987
Gnomad AMR
AF:
0.0985
Gnomad ASJ
AF:
0.119
Gnomad EAS
AF:
0.0328
Gnomad SAS
AF:
0.0984
Gnomad FIN
AF:
0.168
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.140
Gnomad OTH
AF:
0.105
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.109
AC:
16626
AN:
152116
Hom.:
1022
Cov.:
32
AF XY:
0.109
AC XY:
8110
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.0591
Gnomad4 AMR
AF:
0.0983
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.0331
Gnomad4 SAS
AF:
0.0991
Gnomad4 FIN
AF:
0.168
Gnomad4 NFE
AF:
0.140
Gnomad4 OTH
AF:
0.105
Alfa
AF:
0.132
Hom.:
1956
Bravo
AF:
0.102
Asia WGS
AF:
0.0610
AC:
213
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.12
CADD
Benign
22
DANN
Benign
0.69

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: rs11031006; hg19: chr11-30226528; API