6-79915812-CAT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_022726.4(ELOVL4):c.*794_*795del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,490 control chromosomes in the GnomAD database, including 1,902 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.15 (1900 hom., cov: 30)
  • Exomes 𝑓: 0.12 (2 hom.)
• Consequence: ELOVL4 NM_022726.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.57

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 -10 ACMG points.

• BP6: Variant 6-79915812-CAT-C is Benign according to our data. Variant chr6-79915812-CAT-C is described in ClinVar as [Benign]. Clinvar id is 358131.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.*794_*795del		3_prime_UTR_variant	6/6	ENST00000369816.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL4	ENST00000369816.5	c.*794_*795del		3_prime_UTR_variant	6/6	1	NM_022726.4	P1

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22687 AN: 151938 Hom.: 1902 Cov.: 30

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.118 AC: 51 AN: 434 Hom.: 2 AF XY: 0.134 AC XY: 35 AN XY: 262

Gnomad4 FIN exome AF: 0.117

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.149 AC: 22690 AN: 152056 Hom.: 1900 Cov.: 30 AF XY: 0.153 AC XY: 11352 AN XY: 74350

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.156

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: 0.128

Alfa AF: 0.125 Hom.: 152

Bravo AF: 0.150

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Stargardt Disease, Dominant Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs140197858; hg19: chr6-80625529;