NM_017770.4:c.4-15957C>T

Variant names:

• chr6-11026766-G-A
• rs10498676
• NM_017770.4:c.4-15957C>T

Variant summary

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

The NM_017770.4(ELOVL2):​c.4-15957C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,170 control chromosomes in the GnomAD database, including 3,461 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 0.19 (3461 hom., cov: 32)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 11 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL2	NM_017770.4	c.4-15957C>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.4-15957C>T		intron_variant	Intron 1 of 7	1	NM_017770.4	ENSP00000346693.3

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28210 AN: 152052 Hom.: 3461 Cov.: 32

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.185 AC: 28215 AN: 152170 Hom.: 3461 Cov.: 32 AF XY: 0.197 AC XY: 14622 AN XY: 74400

African (AFR) AF: 0.0529 AC: 2199 AN: 41544

American (AMR) AF: 0.281 AC: 4295 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2290 AN: 5178

South Asian (SAS) AF: 0.360 AC: 1735 AN: 4826

European-Finnish (FIN) AF: 0.320 AC: 3376 AN: 10566

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13052 AN: 67984

Other (OTH) AF: 0.165 AC: 349 AN: 2112

Alfa AF: 0.200 Hom.: 1547

Bravo AF: 0.174

Asia WGS AF: 0.360 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.68
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: rs10498676; hg19: chr6-11026999;