15-74203214-TTG-T

Variant summary

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

The ENST00000423167.6(STRA6):c.-15-934_-15-933del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 984,558 control chromosomes in the GnomAD database, including 45,972 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.26 (5861 hom., cov: 24)
  • Exomes 𝑓: 0.31 (40111 hom.)
• Consequence: STRA6 ENST00000423167.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.05

Genes affected

STRA6 (HGNC:30650): (signaling receptor and transporter of retinol STRA6) The protein encoded by this gene is a membrane protein involved in the metabolism of retinol. The encoded protein acts as a receptor for retinol/retinol binding protein complexes. This protein removes the retinol from the complex and transports it across the cell membrane. Defects in this gene are a cause of syndromic microphthalmia type 9 (MCOPS9). Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

CCDC33 (HGNC:26552): (coiled-coil domain containing 33) Predicted to be active in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-74203214-TTG-T is Benign according to our data. Variant chr15-74203214-TTG-T is described in ClinVar as [Benign]. Clinvar id is 1286417.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STRA6	NM_001142617.2	c.-15-934_-15-933del		intron_variant
STRA6	NM_001142619.2	c.-15-934_-15-933del		intron_variant
STRA6	NM_001142620.2	c.-15-934_-15-933del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRA6	ENST00000423167.6	c.-15-934_-15-933del		intron_variant		1
STRA6	ENST00000432245.6	c.-15-934_-15-933del		intron_variant		1
STRA6	ENST00000616000.4			5_prime_UTR_variant	1/19	2		P1

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40088 AN: 151910 Hom.: 5868 Cov.: 24

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.277

GnomAD4 exome AF: 0.309 AC: 256990 AN: 832530 Hom.: 40111 AF XY: 0.309 AC XY: 118748 AN XY: 384464

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.245

Gnomad4 ASJ exome AF: 0.247

Gnomad4 EAS exome AF: 0.440

Gnomad4 SAS exome AF: 0.292

Gnomad4 FIN exome AF: 0.319

Gnomad4 NFE exome AF: 0.313

Gnomad4 OTH exome AF: 0.299

GnomAD4 genome AF: 0.264 AC: 40093 AN: 152028 Hom.: 5861 Cov.: 24 AF XY: 0.264 AC XY: 19636 AN XY: 74296

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.273

Alfa AF: 0.279 Hom.: 782

Bravo AF: 0.257

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs148745262; hg19: chr15-74495555;