Variant 15-74207712-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001199041.2(STRA6):c.15G>A(p.Gly5Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00168 in 1,535,694 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 16 hom., cov: 32)

Exomes 𝑓: 0.0016 ( 54 hom. )

Consequence

STRA6
NM_001199041.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.602

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:

CCDC33 (HGNC:):

CCDC33 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 15-74207712-C-T is Benign according to our data. Variant chr15-74207712-C-T is described in ClinVar as [Benign]. Clinvar id is 1248987.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.602 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein	UniProt
STRA6	NM_001199041.2 linkuse as main transcript	c.15G>A	p.Gly5Gly	synonymous_variant	1/19	NP_001185970.1	Q9BX79-6
STRA6	NM_001199040.2 linkuse as main transcript	c.96+1647G>A		intron_variant		NP_001185969.1	Q9BX79-5
STRA6	NM_001142617.2 linkuse as main transcript	c.-16+1088G>A		intron_variant		NP_001136089.1	Q9BX79-1B3KPB8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
STRA6	ENST00000423167.6 linkuse as main transcript	c.-16+1088G>A		intron_variant		1	ENSP00000413012.2	Q9BX79-3
STRA6	ENST00000432245.6 linkuse as main transcript	c.-16+1088G>A		intron_variant		1	ENSP00000407176.2	Q9BX79-2
STRA6	ENST00000574278.5 linkuse as main transcript	c.15G>A	p.Gly5Gly	synonymous_variant	1/19	2	ENSP00000458827.1	Q9BX79-6

Frequencies

GnomAD3 genomes

AF:

0.00257

AC:

391

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000589

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0700

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00508

AC:

652

AN:

128470

Hom.:

AF XY:

0.00489

AC XY:

344

AN XY:

70350

show subpopulations

Gnomad AFR exome

AF:

0.000163

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0585

Gnomad SAS exome

AF:

0.000893

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000419

Gnomad OTH exome

AF:

0.00450

GnomAD4 exome

AF:

0.00159

AC:

2195

AN:

1383398

Hom.:

Cov.:

AF XY:

0.00159

AC XY:

1085

AN XY:

682598

show subpopulations

Gnomad4 AFR exome

AF:

0.0000633

Gnomad4 AMR exome

AF:

0.0000560

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0501

Gnomad4 SAS exome

AF:

0.00110

Gnomad4 FIN exome

AF:

0.0000299

Gnomad4 NFE exome

AF:

0.0000250

Gnomad4 OTH exome

AF:

0.00487

GnomAD4 genome

AF:

0.00255

AC:

389

AN:

152296

Hom.:

Cov.:

AF XY:

0.00270

AC XY:

201

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.000192

Gnomad4 AMR

AF:

0.000588

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0698

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000294

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.000538

Hom.:

Bravo

AF:

0.00259

Asia WGS

AF:

0.0350

AC:

120

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

May 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.74

DANN

Benign

0.58

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