16-18794363-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000304414.12(ARL6IP1):​c.493+236A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0867 in 152,300 control chromosomes in the GnomAD database, including 691 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.087 ( 691 hom., cov: 33)

Consequence

ARL6IP1
ENST00000304414.12 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.702
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 16-18794363-T-G is Benign according to our data. Variant chr16-18794363-T-G is described in ClinVar as [Benign]. Clinvar id is 1293268.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ARL6IP1NM_015161.3 linkuse as main transcriptc.493+236A>C intron_variant ENST00000304414.12 NP_055976.1
ARL6IP1NM_001313858.1 linkuse as main transcriptc.406+236A>C intron_variant NP_001300787.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ARL6IP1ENST00000304414.12 linkuse as main transcriptc.493+236A>C intron_variant 1 NM_015161.3 ENSP00000306788 P1Q15041-1
ARL6IP1ENST00000563861.5 linkuse as main transcriptc.*75+236A>C intron_variant, NMD_transcript_variant 1 ENSP00000456596
ARL6IP1ENST00000546206.6 linkuse as main transcriptc.406+236A>C intron_variant 2 ENSP00000440048 Q15041-2
ARL6IP1ENST00000562819.5 linkuse as main transcriptc.149-993A>C intron_variant 5 ENSP00000457372

Frequencies

GnomAD3 genomes
AF:
0.0867
AC:
13193
AN:
152182
Hom.:
690
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.152
Gnomad AMI
AF:
0.0691
Gnomad AMR
AF:
0.0560
Gnomad ASJ
AF:
0.0899
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.0312
Gnomad FIN
AF:
0.0429
Gnomad MID
AF:
0.0791
Gnomad NFE
AF:
0.0715
Gnomad OTH
AF:
0.0793
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0867
AC:
13203
AN:
152300
Hom.:
691
Cov.:
33
AF XY:
0.0838
AC XY:
6240
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.152
Gnomad4 AMR
AF:
0.0559
Gnomad4 ASJ
AF:
0.0899
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0313
Gnomad4 FIN
AF:
0.0429
Gnomad4 NFE
AF:
0.0715
Gnomad4 OTH
AF:
0.0784
Alfa
AF:
0.0843
Hom.:
70
Bravo
AF:
0.0903
Asia WGS
AF:
0.0220
AC:
76
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 09, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
7.4
DANN
Benign
0.78

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: rs2641890; hg19: chr16-18805685; API