6-79915941-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_022726.4(ELOVL4):c.*667T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,646 control chromosomes in the GnomAD database, including 2,232 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.16 (2230 hom., cov: 33)
  • Exomes 𝑓: 0.11 (2 hom.)
• Consequence: ELOVL4 NM_022726.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.143

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 6-79915941-A-G is Benign according to our data. Variant chr6-79915941-A-G is described in ClinVar as [Benign]. Clinvar id is 358132.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL4	NM_022726.4	c.*667T>C		3_prime_UTR_variant	6/6	ENST00000369816.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL4	ENST00000369816.5	c.*667T>C		3_prime_UTR_variant	6/6	1	NM_022726.4	P1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24293 AN: 152050 Hom.: 2231 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.113 AC: 54 AN: 476 Hom.: 2 Cov.: 0 AF XY: 0.130 AC XY: 37 AN XY: 284

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.117

Gnomad4 NFE exome AF: 0.0714

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.160 AC: 24310 AN: 152170 Hom.: 2230 Cov.: 33 AF XY: 0.163 AC XY: 12102 AN XY: 74406

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.131

Alfa AF: 0.119 Hom.: 1074

Bravo AF: 0.162

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Stargardt disease 3 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.21
Dann	Benign	0.43

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: rs16891260; hg19: chr6-80625658; COSMIC: COSV63954241;