2-152730385-A-G

Variant names:

• chr2-152730385-A-G
• rs1986743
• NM_152522.7:c.455-4609A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152522.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL6IP6	NM_152522.7	MANE Select	c.455-4609A>G		intron	N/A	NP_689735.1
	ARL6IP6	NM_001371972.1		c.455-4702A>G		intron	N/A	NP_001358901.1
	ARL6IP6	NM_001350068.2		c.167-4609A>G		intron	N/A	NP_001336997.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL6IP6	ENST00000326446.10	TSL:1 MANE Select	c.455-4609A>G		intron	N/A	ENSP00000315357.5
	ARL6IP6	ENST00000688130.1		n.4314A>G		non_coding_transcript_exon	Exon 1 of 2
	ARL6IP6	ENST00000692399.1		c.401-4609A>G		intron	N/A	ENSP00000510087.1

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

African (AFR) AF: 0.651 AC: 26963 AN: 41440

American (AMR) AF: 0.617 AC: 9437 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3470

East Asian (EAS) AF: 0.723 AC: 3729 AN: 5156

South Asian (SAS) AF: 0.571 AC: 2752 AN: 4816

European-Finnish (FIN) AF: 0.779 AC: 8244 AN: 10588

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.673 AC: 45763 AN: 67952

Other (OTH) AF: 0.618 AC: 1306 AN: 2112

Alfa AF: 0.654 Hom.: 41913

Bravo AF: 0.652

Asia WGS AF: 0.599 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.58
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1986743; hg19: chr2-153586899;