Variant 15-74207897-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000423167.6(STRA6):c.-16+903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,489,078 control chromosomes in the GnomAD database, including 45,878 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.22 ( 4016 hom., cov: 32)

Exomes 𝑓: 0.25 ( 41862 hom. )

Consequence

STRA6
ENST00000423167.6 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.55

Variant links:

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]

STRA6 links:

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

CCDC33 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 15-74207897-C-T is Benign according to our data. Variant chr15-74207897-C-T is described in ClinVar as [Benign]. Clinvar id is 675104.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
STRA6	NM_001199041.2 linkuse as main transcript	c.-171G>A	5_prime_UTR_variant	1/19
STRA6	NM_001142617.2 linkuse as main transcript	c.-16+903G>A	intron_variant
STRA6	NM_001142619.2 linkuse as main transcript	c.-16+903G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	UniProt
STRA6	ENST00000423167.6 linkuse as main transcript	c.-16+903G>A	intron_variant		1	Q9BX79-3
STRA6	ENST00000432245.6 linkuse as main transcript	c.-16+903G>A	intron_variant		1	Q9BX79-2
STRA6	ENST00000574278.5 linkuse as main transcript	c.-171G>A	5_prime_UTR_variant	1/19	2	Q9BX79-6

Frequencies

GnomAD3 genomes

AF:

0.223

AC:

33919

AN:

151934

Hom.:

4019

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.233

Gnomad AMR

AF:

0.230

Gnomad ASJ

AF:

0.211

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.239

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.236

GnomAD4 exome

AF:

0.248

AC:

331136

AN:

1337026

Hom.:

41862

Cov.:

AF XY:

0.247

AC XY:

161220

AN XY:

652920

show subpopulations

Gnomad4 AFR exome

AF:

0.145

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.208

Gnomad4 EAS exome

AF:

0.307

Gnomad4 SAS exome

AF:

0.207

Gnomad4 FIN exome

AF:

0.218

Gnomad4 NFE exome

AF:

0.255

Gnomad4 OTH exome

AF:

0.236

GnomAD4 genome

AF:

0.223

AC:

33922

AN:

152052

Hom.:

4016

Cov.:

AF XY:

0.222

AC XY:

16513

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.153

Gnomad4 AMR

AF:

0.230

Gnomad4 ASJ

AF:

0.211

Gnomad4 EAS

AF:

0.282

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.239

Gnomad4 NFE

AF:

0.258

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.234

Hom.:

543

Bravo

AF:

0.220

Asia WGS

AF:

0.237

AC:

825

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.061

DANN

Benign

0.63

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over