rs971756
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000395105.9(STRA6):c.430+24T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,543,242 control chromosomes in the GnomAD database, including 30,271 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.14 ( 2026 hom., cov: 32)
Exomes 𝑓: 0.19 ( 28245 hom. )
Consequence
STRA6
ENST00000395105.9 intron
ENST00000395105.9 intron
Scores
2
12
Clinical Significance
Conservation
PhyloP100: 0.425
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]
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 (MetaRNN=0.003751129).
BP6
Variant 15-74195628-A-T is Benign according to our data. Variant chr15-74195628-A-T is described in ClinVar as [Benign]. Clinvar id is 1183162.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STRA6 | NM_022369.4 | c.430+24T>A | intron_variant | ENST00000395105.9 | NP_071764.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STRA6 | ENST00000395105.9 | c.430+24T>A | intron_variant | 1 | NM_022369.4 | ENSP00000378537 | P1 |
Frequencies
GnomAD3 genomes AF: 0.139 AC: 21038AN: 151704Hom.: 2026 Cov.: 32
GnomAD3 genomes
AF:
AC:
21038
AN:
151704
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.138 AC: 21697AN: 156878Hom.: 2111 AF XY: 0.136 AC XY: 11240AN XY: 82544
GnomAD3 exomes
AF:
AC:
21697
AN:
156878
Hom.:
AF XY:
AC XY:
11240
AN XY:
82544
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.190 AC: 263920AN: 1391420Hom.: 28245 Cov.: 29 AF XY: 0.185 AC XY: 127364AN XY: 686706
GnomAD4 exome
AF:
AC:
263920
AN:
1391420
Hom.:
Cov.:
29
AF XY:
AC XY:
127364
AN XY:
686706
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.139 AC: 21034AN: 151822Hom.: 2026 Cov.: 32 AF XY: 0.137 AC XY: 10125AN XY: 74172
GnomAD4 genome
AF:
AC:
21034
AN:
151822
Hom.:
Cov.:
32
AF XY:
AC XY:
10125
AN XY:
74172
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
823
ALSPAC
AF:
AC:
820
ESP6500AA
AF:
AC:
99
ESP6500EA
AF:
AC:
1006
ExAC
AF:
AC:
5474
Asia WGS
AF:
AC:
82
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:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P;P;P;P;P
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
P
Vest4
ClinPred
T
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at