rs3216411

Variant names:

• chr22-30417563-T-TG
• rs3216411
• NM_012429.5:c.1081+1164dupG

Your query was ambiguous. Multiple possible variants found:

• chr22-30417563-T-TG
• chr22-30417563-T-TGG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_012429.5(SEC14L2):​c.1081+1164dupG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.74 (42315 hom., cov: 0)
• Consequence: SEC14L2 NM_012429.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623
• Publications: 2 publications found

Genes affected

SEC14L2 (HGNC:10699): (SEC14 like lipid binding 2) This gene encodes a cytosolic protein which belongs to a family of lipid-binding proteins including Sec14p, alpha-tocopherol transfer protein, and cellular retinol-binding protein. The encoded protein stimulates squalene monooxygenase which is a downstream enzyme in the cholesterol biosynthetic pathway. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Oct 2008]

ENSG00000249590 (HGNC:):

RNF215 (HGNC:33434): (ring finger protein 215) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in Golgi to vacuole transport; protein targeting to vacuole; and ubiquitin-dependent protein catabolic process. Predicted to be integral component of membrane. Predicted to be part of Golgi transport complex. Predicted to be active in endosome; membrane; and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEC14L2	NM_012429.5	c.1081+1164dupG		intron_variant	Intron 11 of 11	ENST00000615189.5	NP_036561.1
SEC14L2	NM_001291932.2	c.919+1164dupG		intron_variant	Intron 10 of 10		NP_001278861.1
SEC14L2	NM_001204204.3	c.832+1164dupG		intron_variant	Intron 9 of 9		NP_001191133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC14L2	ENST00000615189.5	c.1081+1160_1081+1161insG		intron_variant	Intron 11 of 11	1	NM_012429.5	ENSP00000478755.1
ENSG00000249590	ENST00000439838.5	c.583+1160_583+1161insG		intron_variant	Intron 6 of 8	2		ENSP00000415178.1

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113089 AN: 151932 Hom.: 42279 Cov.: 0

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.744 AC: 113176 AN: 152048 Hom.: 42315 Cov.: 0 AF XY: 0.752 AC XY: 55927 AN XY: 74330

African (AFR) AF: 0.754 AC: 31252 AN: 41462

American (AMR) AF: 0.776 AC: 11862 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2654 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4508 AN: 5166

South Asian (SAS) AF: 0.879 AC: 4235 AN: 4818

European-Finnish (FIN) AF: 0.768 AC: 8122 AN: 10572

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48103 AN: 67962

Other (OTH) AF: 0.759 AC: 1604 AN: 2112

Alfa AF: 0.711 Hom.: 4680

Bravo AF: 0.739

Asia WGS AF: 0.877 AC: 3048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.62
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: rs3216411; hg19: chr22-30813552;