chr16-18793089-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015161.3(ARL6IP1):​c.*163A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0966 in 547,234 control chromosomes in the GnomAD database, including 2,889 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.097 ( 767 hom., cov: 33)
Exomes 𝑓: 0.096 ( 2122 hom. )

Consequence

ARL6IP1
NM_015161.3 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.22
Variant links:
Genes affected
ARL6IP1 (HGNC:697): (ADP ribosylation factor like GTPase 6 interacting protein 1) This gene belongs to the ARL6ip family and encodes a transmembrane protein that is predominantly localized to intracytoplasmic membranes. It is highly expressed in early myeloid progenitor cells and thought to be involved in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. Mutations in this gene are associated with spastic paraplegia 61 (SPG61). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 16-18793089-T-C is Benign according to our data. Variant chr16-18793089-T-C is described in ClinVar as [Benign]. Clinvar id is 1231012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARL6IP1NM_015161.3 linkc.*163A>G 3_prime_UTR_variant Exon 6 of 6 ENST00000304414.12 NP_055976.1 Q15041-1A0A024QYV7
ARL6IP1NM_001313858.1 linkc.*163A>G 3_prime_UTR_variant Exon 6 of 6 NP_001300787.1 Q15041-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ARL6IP1ENST00000304414 linkc.*163A>G 3_prime_UTR_variant Exon 6 of 6 1 NM_015161.3 ENSP00000306788.7 Q15041-1
ENSG00000260342ENST00000567078.2 linkc.493+1510A>G intron_variant Intron 5 of 6 3 ENSP00000454746.2 H3BN98

Frequencies

GnomAD3 genomes
AF:
0.0975
AC:
14836
AN:
152166
Hom.:
769
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0843
Gnomad AMI
AF:
0.0329
Gnomad AMR
AF:
0.149
Gnomad ASJ
AF:
0.180
Gnomad EAS
AF:
0.123
Gnomad SAS
AF:
0.128
Gnomad FIN
AF:
0.0781
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.0885
Gnomad OTH
AF:
0.121
GnomAD4 exome
AF:
0.0962
AC:
37999
AN:
394950
Hom.:
2122
Cov.:
4
AF XY:
0.0984
AC XY:
20756
AN XY:
210962
show subpopulations
Gnomad4 AFR exome
AF:
0.0869
Gnomad4 AMR exome
AF:
0.139
Gnomad4 ASJ exome
AF:
0.174
Gnomad4 EAS exome
AF:
0.0790
Gnomad4 SAS exome
AF:
0.134
Gnomad4 FIN exome
AF:
0.0715
Gnomad4 NFE exome
AF:
0.0879
Gnomad4 OTH exome
AF:
0.108
GnomAD4 genome
AF:
0.0975
AC:
14846
AN:
152284
Hom.:
767
Cov.:
33
AF XY:
0.100
AC XY:
7475
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.0843
Gnomad4 AMR
AF:
0.149
Gnomad4 ASJ
AF:
0.180
Gnomad4 EAS
AF:
0.123
Gnomad4 SAS
AF:
0.127
Gnomad4 FIN
AF:
0.0781
Gnomad4 NFE
AF:
0.0885
Gnomad4 OTH
AF:
0.124
Alfa
AF:
0.0937
Hom.:
712
Bravo
AF:
0.100
Asia WGS
AF:
0.126
AC:
438
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Apr 19, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
0.48
DANN
Benign
0.60
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs11540998; hg19: chr16-18804411; API