ARL6IP6 p.Leu55Leu

Variant names:

• chr2-152718786-C-C
• NM_152522.7:c.

Your query was ambiguous. Multiple possible variants found:

• chr2-152718787--
• chr2-152718787-C-T
• chr2-152718789-G-T
• chr2-152718789-G-C
• chr2-152718789-G-A
• chr2-152718787-CTG-TTA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_152522.7(ARL6IP6):​c. variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ARL6IP6 NM_152522.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL6IP6	NM_152522.7	MANE Select	c.		intron	N/A	NP_689735.1	Q8N6S5
	ARL6IP6	NM_001371972.1		c.		intron	N/A	NP_001358901.1	A0A8I5KQ30
	ARL6IP6	NM_001350068.2		c.		intron	N/A	NP_001336997.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL6IP6	ENST00000326446.10	TSL:1 MANE Select	c.		intron	N/A	ENSP00000315357.5	Q8N6S5
	ARL6IP6	ENST00000463690.2	TSL:2	c.		exon_region	Exon 1 of 3	ENSP00000508954.1	A0A8I5QJ95
	ARL6IP6	ENST00000463690.2	TSL:2	c.		5_prime_UTR	Exon 1 of 3	ENSP00000508954.1	A0A8I5QJ95

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.078

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr2-153575300;