6-11005453-G-A

Position:

• chr6-11005453-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017770.4(ELOVL2):​c.174C>T​(p.Asn58Asn) variant causes a synonymous change. The variant allele was found at a frequency of 0.226 in 1,613,114 control chromosomes in the GnomAD database, including 42,253 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 0.21 (3444 hom., cov: 32)
  • Exomes 𝑓: 0.23 (38809 hom.)
• Consequence: ELOVL2 NM_017770.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.68

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELOVL2	NM_017770.4	c.174C>T	p.Asn58Asn	synonymous_variant	3/8	ENST00000354666.4	NP_060240.3
ELOVL2	XM_011514716.4	c.264C>T	p.Asn88Asn	synonymous_variant	3/8		XP_011513018.1
ELOVL2	XM_011514717.4	c.177C>T	p.Asn59Asn	synonymous_variant	3/8		XP_011513019.1
ELOVL2	XM_017010985.2	c.264C>T	p.Asn88Asn	synonymous_variant	3/5		XP_016866474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELOVL2	ENST00000354666.4	c.174C>T	p.Asn58Asn	synonymous_variant	3/8	1	NM_017770.4	ENSP00000346693.3

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31824 AN: 151970 Hom.: 3438 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.256

GnomAD3 exomes AF: 0.221 AC: 55360 AN: 251036 Hom.: 6355 AF XY: 0.223 AC XY: 30209 AN XY: 135714

Gnomad AFR exome AF: 0.163

Gnomad AMR exome AF: 0.224

Gnomad ASJ exome AF: 0.313

Gnomad EAS exome AF: 0.278

Gnomad SAS exome AF: 0.224

Gnomad FIN exome AF: 0.114

Gnomad NFE exome AF: 0.229

Gnomad OTH exome AF: 0.230

GnomAD4 exome AF: 0.228 AC: 332967 AN: 1461026 Hom.: 38809 Cov.: 33 AF XY: 0.228 AC XY: 165838 AN XY: 726846

Gnomad4 AFR exome AF: 0.157

Gnomad4 AMR exome AF: 0.230

Gnomad4 ASJ exome AF: 0.317

Gnomad4 EAS exome AF: 0.269

Gnomad4 SAS exome AF: 0.224

Gnomad4 FIN exome AF: 0.119

Gnomad4 NFE exome AF: 0.231

Gnomad4 OTH exome AF: 0.244

GnomAD4 genome AF: 0.209 AC: 31850 AN: 152088 Hom.: 3444 Cov.: 32 AF XY: 0.205 AC XY: 15223 AN XY: 74334

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.261

Alfa AF: 0.226 Hom.: 2346

Bravo AF: 0.217

Asia WGS AF: 0.265 AC: 925 AN: 3478

EpiCase AF: 0.240

EpiControl AF: 0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	9.3
DANN	Benign	0.62

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: rs2295601; hg19: chr6-11005686; COSMIC: COSV61154168;