6-10980820-G-A

Position:

• chr6-10980820-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.*2961C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,466 control chromosomes in the GnomAD database, including 22,598 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 0.53 (22557 hom., cov: 32)
  • Exomes 𝑓: 0.45 (41 hom.)
• Consequence: ELOVL2 NM_017770.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80

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=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELOVL2	NM_017770.4	c.*2961C>T		3_prime_UTR_variant	8/8	ENST00000354666.4	NP_060240.3
ELOVL2	XM_011514716.4	c.*2961C>T		3_prime_UTR_variant	8/8		XP_011513018.1
ELOVL2	XM_011514717.4	c.*2961C>T		3_prime_UTR_variant	8/8		XP_011513019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELOVL2	ENST00000354666.4	c.*2961C>T		3_prime_UTR_variant	8/8	1	NM_017770.4	ENSP00000346693	P1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80827 AN: 151918 Hom.: 22519 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.515

GnomAD4 exome AF: 0.449 AC: 193 AN: 430 Hom.: 41 Cov.: 0 AF XY: 0.438 AC XY: 113 AN XY: 258

Gnomad4 FIN exome AF: 0.446

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.532 AC: 80919 AN: 152036 Hom.: 22557 Cov.: 32 AF XY: 0.540 AC XY: 40164 AN XY: 74312

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.519

Alfa AF: 0.461 Hom.: 25309

Bravo AF: 0.545

Asia WGS AF: 0.773 AC: 2685 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	14
DANN	Benign	0.73

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: rs8523; hg19: chr6-10981053; COSMIC: COSV61157711; COSMIC: COSV61157711;