rs9997926

Positions:

• chr4-110055923-C-T

Variant summary

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

The NM_024090.3(ELOVL6):​c.373+3680G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 152,056 control chromosomes in the GnomAD database, including 553 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 0.082 (553 hom., cov: 31)
• Consequence: ELOVL6 NM_024090.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

Genes affected

ELOVL6 (HGNC:15829): (ELOVL fatty acid elongase 6) Fatty acid elongases (EC 6.2.1.3), such as ELOVL6, use malonyl-CoA as a 2-carbon donor in the first and rate-limiting step of fatty acid elongation (Moon et al., 2001 [PubMed 11567032]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL6	NM_024090.3	c.373+3680G>A		intron_variant		ENST00000302274.8
ELOVL6	NM_001130721.2	c.373+3680G>A		intron_variant
ELOVL6	XM_011532233.4	c.373+3680G>A		intron_variant
ELOVL6	XM_011532234.4	c.373+3680G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL6	ENST00000302274.8	c.373+3680G>A		intron_variant		2	NM_024090.3	P1

Frequencies

GnomAD3 genomes AF: 0.0819 AC: 12449 AN: 151938 Hom.: 552 Cov.: 31

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.0809

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.0753

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

GnomAD4 genome AF: 0.0818 AC: 12445 AN: 152056 Hom.: 553 Cov.: 31 AF XY: 0.0794 AC XY: 5902 AN XY: 74344

Gnomad4 AFR AF: 0.0941

Gnomad4 AMR AF: 0.0645

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0206

Gnomad4 FIN AF: 0.0809

Gnomad4 NFE AF: 0.0869

Gnomad4 OTH AF: 0.0745

Alfa AF: 0.0834 Hom.: 253

Bravo AF: 0.0830

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.3
DANN	Benign	0.70

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: rs9997926; hg19: chr4-110977079;