rs3756963

Positions:

• chr6-11021921-T-C
• chr6-11021921-T-G

Variant summary

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

The NM_017770.4(ELOVL2):​c.4-11112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,880 control chromosomes in the GnomAD database, including 4,400 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 0.24 (4400 hom., cov: 31)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELOVL2	NM_017770.4	c.4-11112A>G		intron_variant		ENST00000354666.4	NP_060240.3
ELOVL2	XM_011514716.4	c.-9944A>G		5_prime_UTR_variant	1/8		XP_011513018.1
ELOVL2	XM_011514717.4	c.-9434A>G		5_prime_UTR_variant	1/8		XP_011513019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELOVL2	ENST00000354666.4	c.4-11112A>G		intron_variant		1	NM_017770.4	ENSP00000346693	P1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36294 AN: 151762 Hom.: 4395 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.239 AC: 36326 AN: 151880 Hom.: 4400 Cov.: 31 AF XY: 0.233 AC XY: 17314 AN XY: 74204

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.289

Alfa AF: 0.252 Hom.: 8396

Bravo AF: 0.249

Asia WGS AF: 0.274 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.51

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: rs3756963; hg19: chr6-11022154;