rs1986743

chr2-152730385-A-Gchr2-152730385-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152522.7(ARL6IP6):c.455-4609A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,024 control chromosomes in the GnomAD database, including 33,514 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 0.66 (33514 hom., cov: 31)
• Consequence: ARL6IP6 NM_152522.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313

Genes affected

ARL6IP6 (HGNC:24048): (ADP ribosylation factor like GTPase 6 interacting protein 6) Predicted to be located in nuclear inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL6IP6	NM_152522.7	c.455-4609A>G		intron_variant		ENST00000326446.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL6IP6	ENST00000326446.10	c.455-4609A>G		intron_variant		1	NM_152522.7	P1

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100546 AN: 151904 Hom.: 33496 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.625

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.662 AC: 100614 AN: 152024 Hom.: 33514 Cov.: 31 AF XY: 0.663 AC XY: 49298 AN XY: 74304

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.618

Alfa AF: 0.655 Hom.: 32023

Bravo AF: 0.652

Asia WGS AF: 0.599 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.0
Dann	Benign	0.58

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

Other links and lift over

dbSNP: rs1986743; hg19: chr2-153586899;