Variant rs12913041 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_022369.4(STRA6):c.1685-24T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,612,240 control chromosomes in the GnomAD database, including 32,650 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2273 hom., cov: 31)

Exomes 𝑓: 0.19 ( 30377 hom. )

Consequence

STRA6
NM_022369.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0960

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 15-74180961-A-G is Benign according to our data. Variant chr15-74180961-A-G is described in ClinVar as [Benign]. Clinvar id is 1239030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STRA6	NM_022369.4 linkuse as main transcript	c.1685-24T>C		intron_variant		ENST00000395105.9	NP_071764.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STRA6	ENST00000395105.9 linkuse as main transcript	c.1685-24T>C		intron_variant		1	NM_022369.4	ENSP00000378537	P1	Q9BX79-1

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22970

AN:

151844

Hom.:

2270

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0676

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.0928

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.00136

Gnomad SAS

AF:

0.0332

Gnomad FIN

AF:

0.275

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.127

GnomAD3 exomes

AF:

0.150

AC:

37314

AN:

249202

Hom.:

3801

AF XY:

0.149

AC XY:

20063

AN XY:

134700

show subpopulations

Gnomad AFR exome

AF:

0.0656

Gnomad AMR exome

AF:

0.0684

Gnomad ASJ exome

AF:

0.203

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0467

Gnomad FIN exome

AF:

0.275

Gnomad NFE exome

AF:

0.210

Gnomad OTH exome

AF:

0.161

GnomAD4 exome

AF:

0.192

AC:

280579

AN:

1460278

Hom.:

30377

Cov.:

AF XY:

0.188

AC XY:

136425

AN XY:

726264

show subpopulations

Gnomad4 AFR exome

AF:

0.0619

Gnomad4 AMR exome

AF:

0.0684

Gnomad4 ASJ exome

AF:

0.207

Gnomad4 EAS exome

AF:

0.000252

Gnomad4 SAS exome

AF:

0.0489

Gnomad4 FIN exome

AF:

0.283

Gnomad4 NFE exome

AF:

0.216

Gnomad4 OTH exome

AF:

0.177

GnomAD4 genome

AF:

0.151

AC:

22979

AN:

151962

Hom.:

2273

Cov.:

AF XY:

0.150

AC XY:

11109

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.0677

Gnomad4 AMR

AF:

0.0926

Gnomad4 ASJ

AF:

0.209

Gnomad4 EAS

AF:

0.00136

Gnomad4 SAS

AF:

0.0324

Gnomad4 FIN

AF:

0.275

Gnomad4 NFE

AF:

0.214

Gnomad4 OTH

AF:

0.126

Alfa

AF:

0.190

Hom.:

598

Bravo

AF:

0.134

Asia WGS

AF:

0.0300

AC:

104

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.7

DANN

Benign

0.29

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

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