dbSNP rs351224: STRA6:c.*907A>T (chr15-74194695-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000432245.6(STRA6):c.*907A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 1,090,198 control chromosomes in the GnomAD database, including 116,914 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.46 ( 16650 hom., cov: 32)

Exomes 𝑓: 0.46 ( 100264 hom. )

Consequence

STRA6
ENST00000432245.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.264

Publications

13 publications found

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 Gene-Disease associations (from GenCC):

Matthew-Wood syndrome
Inheritance: AR, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae), Orphanet
microphthalmia, isolated, with coloboma
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

STRA6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STRA6	NM_022369.4 link	c.597+607A>T		intron_variant	Intron 7 of 18	ENST00000395105.9	NP_071764.3	Q9BX79-1B3KPB8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STRA6	ENST00000395105.9 link	c.597+607A>T		intron_variant	Intron 7 of 18	1	NM_022369.4	ENSP00000378537.4		Q9BX79-1

Frequencies

GnomAD3 genomes

AF:

0.463

AC:

70277

AN:

151916

Hom.:

16630

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.496

Gnomad AMR

AF:

0.603

Gnomad ASJ

AF:

0.519

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.589

Gnomad FIN

AF:

0.411

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.450

Gnomad OTH

AF:

0.513

GnomAD4 exome

AF:

0.460

AC:

431602

AN:

938164

Hom.:

100264

Cov.:

AF XY:

0.461

AC XY:

206510

AN XY:

447936

show subpopulations

African (AFR)

AF:

0.416

AC:

8333

AN:

20026

American (AMR)

AF:

0.638

AC:

7082

AN:

11094

Ashkenazi Jewish (ASJ)

AF:

0.526

AC:

7160

AN:

13620

East Asian (EAS)

AF:

0.547

AC:

14602

AN:

26698

South Asian (SAS)

AF:

0.579

AC:

10058

AN:

17364

European-Finnish (FIN)

AF:

0.414

AC:

8830

AN:

21346

Middle Eastern (MID)

AF:

0.536

AC:

1413

AN:

2634

European-Non Finnish (NFE)

AF:

0.452

AC:

355125

AN:

785944

Other (OTH)

AF:

0.482

AC:

18999

AN:

39438

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

11186

22372

33558

44744

55930

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11940

23880

35820

47760

59700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.463

AC:

70337

AN:

152034

Hom.:

16650

Cov.:

AF XY:

0.467

AC XY:

34692

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.416

AC:

17248

AN:

41456

American (AMR)

AF:

0.603

AC:

9205

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.519

AC:

1801

AN:

3470

East Asian (EAS)

AF:

0.510

AC:

2640

AN:

5178

South Asian (SAS)

AF:

0.590

AC:

2836

AN:

4806

European-Finnish (FIN)

AF:

0.411

AC:

4343

AN:

10576

Middle Eastern (MID)

AF:

0.558

AC:

164

AN:

294

European-Non Finnish (NFE)

AF:

0.450

AC:

30550

AN:

67956

Other (OTH)

AF:

0.519

AC:

1098

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1963

3927

5890

7854

9817

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

644

1288

1932

2576

3220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.448

Hom.:

1954

Bravo

AF:

0.474

Asia WGS

AF:

0.543

AC:

1893

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.2

(source)

DANN

Benign

0.86

PhyloP100

0.26

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over