chr4-110161014-C-T

Position:

• chr4-110161014-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.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

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=-0.9).
• 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/exons	MANE	UniProt
ELOVL6	NM_024090.3	c.89+37233G>A		intron_variant		ENST00000302274.8
ELOVL6	NM_001130721.2	c.89+37233G>A		intron_variant
ELOVL6	XM_011532233.4	c.89+37233G>A		intron_variant
ELOVL6	XM_011532234.4	c.89+37233G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL6	ENST00000302274.8	c.89+37233G>A		intron_variant		2	NM_024090.3	P1

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

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.562

Alfa AF: 0.516 Hom.: 2982

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

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: rs7681062; hg19: chr4-111082170;