2-152721872-C-T

Variant names:

• chr2-152721872-C-T
• rs4233660
• NM_152522.7:c.454+1286C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152522.7(ARL6IP6):​c.454+1286C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,134 control chromosomes in the GnomAD database, including 30,323 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 0.63 (30323 hom., cov: 34)
• Consequence: ARL6IP6 NM_152522.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL6IP6	NM_152522.7	c.454+1286C>T		intron_variant	Intron 2 of 3	ENST00000326446.10	NP_689735.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL6IP6	ENST00000326446.10	c.454+1286C>T		intron_variant	Intron 2 of 3	1	NM_152522.7	ENSP00000315357.5

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95124 AN: 152016 Hom.: 30312 Cov.: 34

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.626 AC: 95179 AN: 152134 Hom.: 30323 Cov.: 34 AF XY: 0.628 AC XY: 46735 AN XY: 74380

African (AFR) AF: 0.526 AC: 21797 AN: 41468

American (AMR) AF: 0.603 AC: 9221 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3472

East Asian (EAS) AF: 0.720 AC: 3727 AN: 5176

South Asian (SAS) AF: 0.574 AC: 2772 AN: 4830

European-Finnish (FIN) AF: 0.780 AC: 8261 AN: 10588

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45736 AN: 67998

Other (OTH) AF: 0.587 AC: 1241 AN: 2114

Alfa AF: 0.652 Hom.: 6821

Bravo AF: 0.611

Asia WGS AF: 0.592 AC: 2056 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	3.6
DANN	Benign	0.40
PhyloP100		-0.42
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: rs4233660; hg19: chr2-153578386;