rs971757

chr15-74195505-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000432245.6(STRA6):c.*97C>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 0.184 in 1,607,720 control chromosomes in the GnomAD database, including 31,265 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.14 (2021 hom., cov: 31)
  • Exomes 𝑓: 0.19 (29244 hom.)
• Consequence: STRA6 ENST00000432245.6 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.724

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 15-74195505-G-A is Benign according to our data. Variant chr15-74195505-G-A is described in ClinVar as [Benign]. Clinvar id is 1294251.Status of the report is criteria_provided_single_submitter, 1 stars.
• 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	UniProt
STRA6	NM_022369.4	c.431-37C>T		intron_variant		ENST00000395105.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STRA6	ENST00000395105.9	c.431-37C>T		intron_variant		1	NM_022369.4	P1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21022 AN: 151906 Hom.: 2021 Cov.: 31

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.00136

Gnomad SAS AF: 0.0322

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.114

GnomAD3 exomes AF: 0.144 AC: 34158 AN: 237372 Hom.: 3346 AF XY: 0.144 AC XY: 18433 AN XY: 127930

Gnomad AFR exome AF: 0.0334

Gnomad AMR exome AF: 0.0650

Gnomad ASJ exome AF: 0.181

Gnomad EAS exome AF: 0.000287

Gnomad SAS exome AF: 0.0459

Gnomad FIN exome AF: 0.259

Gnomad NFE exome AF: 0.208

Gnomad OTH exome AF: 0.157

GnomAD4 exome AF: 0.188 AC: 274329 AN: 1455696 Hom.: 29244 Cov.: 33 AF XY: 0.184 AC XY: 133307 AN XY: 723412

Gnomad4 AFR exome AF: 0.0277

Gnomad4 AMR exome AF: 0.0661

Gnomad4 ASJ exome AF: 0.185

Gnomad4 EAS exome AF: 0.000279

Gnomad4 SAS exome AF: 0.0472

Gnomad4 FIN exome AF: 0.264

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.169

GnomAD4 genome AF: 0.138 AC: 21018 AN: 152024 Hom.: 2021 Cov.: 31 AF XY: 0.136 AC XY: 10115 AN XY: 74284

Gnomad4 AFR AF: 0.0367

Gnomad4 AMR AF: 0.0859

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.00136

Gnomad4 SAS AF: 0.0316

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.113

Alfa AF: 0.178 Hom.: 552

Bravo AF: 0.121

Asia WGS AF: 0.0240 AC: 82 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	-0.89
Cadd	Benign	1.1
Dann	Benign	0.50

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

LitVar

Other links and lift over

dbSNP: rs971757; hg19: chr15-74487846; COSMIC: COSV60588017; COSMIC: COSV60588017;