rs2450

Positions:

• chr2-152727907-T-G

Variant summary

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

The NM_152522.7(ARL6IP6):​c.455-7087T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,192 control chromosomes in the GnomAD database, including 4,030 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 0.20 (4030 hom., cov: 32)
• Consequence: ARL6IP6 NM_152522.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARL6IP6	NM_152522.7	c.455-7087T>G		intron_variant		ENST00000326446.10	NP_689735.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARL6IP6	ENST00000326446.10	c.455-7087T>G		intron_variant		1	NM_152522.7	ENSP00000315357	P1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30819 AN: 152074 Hom.: 4031 Cov.: 32

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.203 AC: 30825 AN: 152192 Hom.: 4030 Cov.: 32 AF XY: 0.196 AC XY: 14588 AN XY: 74412

Gnomad4 AFR AF: 0.0611

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.184

Alfa AF: 0.228 Hom.: 835

Bravo AF: 0.195

Asia WGS AF: 0.101 AC: 353 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.56

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: rs2450; hg19: chr2-153584421;