rs11857410

Positions:

chr15-74196083-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_022369.4(STRA6):c.331C>T(p.Leu111Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,613,882 control chromosomes in the GnomAD database, including 31,538 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2096 hom., cov: 32)

Exomes 𝑓: 0.19 ( 29442 hom. )

Consequence

STRA6
NM_022369.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 3.19

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 15-74196083-G-A is Benign according to our data. Variant chr15-74196083-G-A is described in ClinVar as [Benign]. Clinvar id is 317117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=3.19 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 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.331C>T	p.Leu111Leu	synonymous_variant	5/19	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.331C>T	p.Leu111Leu	synonymous_variant	5/19	1	NM_022369.4	ENSP00000378537.4		Q9BX79-1

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22151

AN:

152026

Hom.:

2096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0624

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.0878

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0323

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.120

GnomAD3 exomes

AF:

0.145

AC:

36275

AN:

250618

Hom.:

3577

AF XY:

0.144

AC XY:

19536

AN XY:

135574

show subpopulations

Gnomad AFR exome

AF:

0.0614

Gnomad AMR exome

AF:

0.0655

Gnomad ASJ exome

AF:

0.181

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0455

Gnomad FIN exome

AF:

0.256

Gnomad NFE exome

AF:

0.206

Gnomad OTH exome

AF:

0.154

GnomAD4 exome

AF:

0.189

AC:

276193

AN:

1461738

Hom.:

29442

Cov.:

AF XY:

0.185

AC XY:

134226

AN XY:

727152

show subpopulations

Gnomad4 AFR exome

AF:

0.0534

Gnomad4 AMR exome

AF:

0.0669

Gnomad4 ASJ exome

AF:

0.185

Gnomad4 EAS exome

AF:

0.000277

Gnomad4 SAS exome

AF:

0.0472

Gnomad4 FIN exome

AF:

0.264

Gnomad4 NFE exome

AF:

0.214

Gnomad4 OTH exome

AF:

0.170

GnomAD4 genome

AF:

0.146

AC:

22147

AN:

152144

Hom.:

2096

Cov.:

AF XY:

0.143

AC XY:

10654

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.0622

Gnomad4 AMR

AF:

0.0877

Gnomad4 ASJ

AF:

0.187

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0317

Gnomad4 FIN

AF:

0.258

Gnomad4 NFE

AF:

0.210

Gnomad4 OTH

AF:

0.118

Alfa

AF:

0.186

Hom.:

5735

Bravo

AF:

0.129

Asia WGS

AF:

0.0270

AC:

AN:

3478

EpiCase

AF:

0.186

EpiControl

AF:

0.182

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Matthew-Wood syndrome

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 22, 2024	- -

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

-0.66

CADD

Benign

8.9

DANN

Benign

0.74

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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