rs17239120

Positions:

• chr6-79942185-G-C

Variant summary

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

The NM_022726.4(ELOVL4):​c.100+4995C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0622 in 152,230 control chromosomes in the GnomAD database, including 396 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 0.062 (396 hom., cov: 32)
• Consequence: ELOVL4 NM_022726.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

ELOVL4 (HGNC:14415): (ELOVL fatty acid elongase 4) This gene encodes a membrane-bound protein which is a member of the ELO family, proteins which participate in the biosynthesis of fatty acids. Consistent with the expression of the encoded protein in photoreceptor cells of the retina, mutations and small deletions in this gene are associated with Stargardt-like macular dystrophy (STGD3) and autosomal dominant Stargardt-like macular dystrophy (ADMD), also referred to as autosomal dominant atrophic macular degeneration. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL4	NM_022726.4	c.100+4995C>G		intron_variant		ENST00000369816.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL4	ENST00000369816.5	c.100+4995C>G		intron_variant		1	NM_022726.4	P1

Frequencies

GnomAD3 genomes AF: 0.0622 AC: 9460 AN: 152112 Hom.: 396 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0918

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.0573

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

GnomAD4 genome AF: 0.0622 AC: 9464 AN: 152230 Hom.: 396 Cov.: 32 AF XY: 0.0654 AC XY: 4870 AN XY: 74442

Gnomad4 AFR AF: 0.0138

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.0662

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0918

Gnomad4 NFE AF: 0.0714

Gnomad4 OTH AF: 0.0581

Alfa AF: 0.0645 Hom.: 43

Bravo AF: 0.0602

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.61

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: rs17239120; hg19: chr6-80651902;