4-110161014-C-T

Variant names:

• chr4-110161014-C-T
• rs7681062
• NM_024090.3:c.89+37233G>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.89+37233G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,018 control chromosomes in the GnomAD database, including 24,487 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 0.56 (24487 hom., cov: 33)
• Consequence: ELOVL6 NM_024090.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL6	NM_024090.3	c.89+37233G>A		intron_variant	Intron 1 of 3	ENST00000302274.8	NP_076995.1
ELOVL6	NM_001130721.2	c.89+37233G>A		intron_variant	Intron 2 of 4		NP_001124193.1
ELOVL6	XM_011532233.4	c.89+37233G>A		intron_variant	Intron 2 of 4		XP_011530535.1
ELOVL6	XM_011532234.4	c.89+37233G>A		intron_variant	Intron 2 of 4		XP_011530536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL6	ENST00000302274.8	c.89+37233G>A		intron_variant	Intron 1 of 3	2	NM_024090.3	ENSP00000304736.3

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85750 AN: 151902 Hom.: 24464 Cov.: 33

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.565 AC: 85818 AN: 152018 Hom.: 24487 Cov.: 33 AF XY: 0.566 AC XY: 42038 AN XY: 74290

African (AFR) AF: 0.537 AC: 22234 AN: 41440

American (AMR) AF: 0.589 AC: 8989 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1672 AN: 3470

East Asian (EAS) AF: 0.781 AC: 4045 AN: 5180

South Asian (SAS) AF: 0.430 AC: 2071 AN: 4818

European-Finnish (FIN) AF: 0.582 AC: 6149 AN: 10560

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38707 AN: 67968

Other (OTH) AF: 0.562 AC: 1189 AN: 2114

Alfa AF: 0.517 Hom.: 3102

Bravo AF: 0.568

Asia WGS AF: 0.553 AC: 1918 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.27
PhyloP100		-0.87
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: rs7681062; hg19: chr4-111082170;