rs9997926

Variant names:

• chr4-110055923-C-T
• rs9997926
• NM_024090.3:c.373+3680G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ELOVL6	NM_024090.3	c.373+3680G>A		intron_variant	Intron 3 of 3	ENST00000302274.8	NP_076995.1
ELOVL6	NM_001130721.2	c.373+3680G>A		intron_variant	Intron 4 of 4		NP_001124193.1
ELOVL6	XM_011532233.4	c.373+3680G>A		intron_variant	Intron 4 of 4		XP_011530535.1
ELOVL6	XM_011532234.4	c.373+3680G>A		intron_variant	Intron 4 of 4		XP_011530536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL6	ENST00000302274.8	c.373+3680G>A		intron_variant	Intron 3 of 3	2	NM_024090.3	ENSP00000304736.3

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

African (AFR) AF: 0.0941 AC: 3901 AN: 41450

American (AMR) AF: 0.0645 AC: 986 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.0206 AC: 99 AN: 4816

European-Finnish (FIN) AF: 0.0809 AC: 854 AN: 10560

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0869 AC: 5911 AN: 67982

Other (OTH) AF: 0.0745 AC: 157 AN: 2108

Alfa AF: 0.0845 Hom.: 293

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
PhyloP100		-0.81
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: rs9997926; hg19: chr4-110977079;