rs953413

Variant names:

• chr6-11012626-G-A
• rs953413
• NM_017770.4:c.4-1817C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-11012626-G-A
• chr6-11012626-G-C

Variant summary

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

The NM_017770.4(ELOVL2):​c.4-1817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,084 control chromosomes in the GnomAD database, including 24,091 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 0.55 (24091 hom., cov: 33)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 32 publications found

Genes affected

ELOVL2 (HGNC:14416): (ELOVL fatty acid elongase 2) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated fatty acid and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL2	NM_017770.4	c.4-1817C>T		intron_variant	Intron 1 of 7	ENST00000354666.4	NP_060240.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL2	ENST00000354666.4	c.4-1817C>T		intron_variant	Intron 1 of 7	1	NM_017770.4	ENSP00000346693.3

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83269 AN: 151966 Hom.: 24041 Cov.: 33

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.548 AC: 83376 AN: 152084 Hom.: 24091 Cov.: 33 AF XY: 0.554 AC XY: 41215 AN XY: 74338

African (AFR) AF: 0.664 AC: 27530 AN: 41482

American (AMR) AF: 0.637 AC: 9740 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1932 AN: 3470

East Asian (EAS) AF: 0.905 AC: 4692 AN: 5182

South Asian (SAS) AF: 0.662 AC: 3199 AN: 4830

European-Finnish (FIN) AF: 0.480 AC: 5062 AN: 10548

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.436 AC: 29649 AN: 67976

Other (OTH) AF: 0.542 AC: 1145 AN: 2112

Alfa AF: 0.484 Hom.: 10647

Bravo AF: 0.565

Asia WGS AF: 0.754 AC: 2619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.28
DANN	Benign	0.85
PhyloP100		-2.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs953413; hg19: chr6-11012859;