rs3798719

Variant names:

• chr6-11036592-C-T
• rs3798719
• NM_017770.4:c.3+7636G>A

Variant summary

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

The NM_017770.4(ELOVL2):​c.3+7636G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,150 control chromosomes in the GnomAD database, including 3,142 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 0.18 (3142 hom., cov: 32)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.900
• Publications: 12 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL2	NM_017770.4	c.3+7636G>A		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.3+7636G>A		intron_variant	Intron 1 of 7	1	NM_017770.4	ENSP00000346693.3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27474 AN: 152030 Hom.: 3137 Cov.: 32

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.181 AC: 27480 AN: 152150 Hom.: 3142 Cov.: 32 AF XY: 0.178 AC XY: 13247 AN XY: 74382

African (AFR) AF: 0.0456 AC: 1894 AN: 41546

American (AMR) AF: 0.250 AC: 3818 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1381 AN: 5174

South Asian (SAS) AF: 0.245 AC: 1181 AN: 4820

European-Finnish (FIN) AF: 0.111 AC: 1176 AN: 10580

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16101 AN: 67982

Other (OTH) AF: 0.241 AC: 508 AN: 2108

Alfa AF: 0.225 Hom.: 1724

Bravo AF: 0.183

Asia WGS AF: 0.256 AC: 894 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	9.4
DANN	Benign	0.59
PhyloP100		0.90
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: rs3798719; hg19: chr6-11036825;