Variant 15-74180732-A-G 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.1840+50T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 1,563,154 control chromosomes in the GnomAD database, including 31,903 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2276 hom., cov: 31)

Exomes 𝑓: 0.19 ( 29627 hom. )

Consequence

STRA6
NM_022369.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.329

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:

STRA6 (HGNC:):

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=-0.9).

BP6

Variant 15-74180732-A-G is Benign according to our data. Variant chr15-74180732-A-G is described in ClinVar as [Benign]. Clinvar id is 1265464.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 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.1840+50T>C		intron_variant		ENST00000395105.9	NP_071764.3	Q9BX79-1B3KPB8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STRA6	ENST00000395105.9 linkuse as main transcript	c.1840+50T>C		intron_variant		1	NM_022369.4	ENSP00000378537.4		Q9BX79-1

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22938

AN:

151922

Hom.:

2273

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0658

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.0937

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0326

Gnomad FIN

AF:

0.275

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.215

Gnomad OTH

AF:

0.129

GnomAD3 exomes

AF:

0.151

AC:

33850

AN:

223636

Hom.:

3465

AF XY:

0.151

AC XY:

18241

AN XY:

120486

show subpopulations

Gnomad AFR exome

AF:

0.0637

Gnomad AMR exome

AF:

0.0703

Gnomad ASJ exome

AF:

0.206

Gnomad EAS exome

AF:

0.000280

Gnomad SAS exome

AF:

0.0458

Gnomad FIN exome

AF:

0.276

Gnomad NFE exome

AF:

0.211

Gnomad OTH exome

AF:

0.164

GnomAD4 exome

AF:

0.193

AC:

272822

AN:

1411112

Hom.:

29627

Cov.:

AF XY:

0.189

AC XY:

131495

AN XY:

695182

show subpopulations

Gnomad4 AFR exome

AF:

0.0599

Gnomad4 AMR exome

AF:

0.0701

Gnomad4 ASJ exome

AF:

0.207

Gnomad4 EAS exome

AF:

0.000257

Gnomad4 SAS exome

AF:

0.0488

Gnomad4 FIN exome

AF:

0.283

Gnomad4 NFE exome

AF:

0.216

Gnomad4 OTH exome

AF:

0.177

GnomAD4 genome

AF:

0.151

AC:

22947

AN:

152042

Hom.:

2276

Cov.:

AF XY:

0.149

AC XY:

11095

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.0659

Gnomad4 AMR

AF:

0.0935

Gnomad4 ASJ

AF:

0.209

Gnomad4 EAS

AF:

0.00136

Gnomad4 SAS

AF:

0.0318

Gnomad4 FIN

AF:

0.275

Gnomad4 NFE

AF:

0.215

Gnomad4 OTH

AF:

0.127

Alfa

AF:

0.143

Hom.:

518

Bravo

AF:

0.134

Asia WGS

AF:

0.0300

AC:

103

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

-0.90

CADD

Benign

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

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