rs201408425
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_022369.4(STRA6):āc.1391T>Gā(p.Leu464Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000153 in 1,614,028 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00022 ( 1 hom., cov: 32)
Exomes š: 0.00015 ( 3 hom. )
Consequence
STRA6
NM_022369.4 missense
NM_022369.4 missense
Scores
2
10
6
Clinical Significance
Conservation
PhyloP100: 4.13
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.06258991).
BP6
?
Variant 15-74182370-A-C is Benign according to our data. Variant chr15-74182370-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 464031.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000217 (33/152304) while in subpopulation AMR AF= 0.00183 (28/15306). AF 95% confidence interval is 0.0013. There are 1 homozygotes in gnomad4. There are 10 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STRA6 | NM_022369.4 | c.1391T>G | p.Leu464Arg | missense_variant | 15/19 | ENST00000395105.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRA6 | ENST00000395105.9 | c.1391T>G | p.Leu464Arg | missense_variant | 15/19 | 1 | NM_022369.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152186Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000590 AC: 148AN: 250932Hom.: 2 AF XY: 0.000442 AC XY: 60AN XY: 135666
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GnomAD4 exome AF: 0.000146 AC: 214AN: 1461724Hom.: 3 Cov.: 31 AF XY: 0.000125 AC XY: 91AN XY: 727150
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GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152304Hom.: 1 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74486
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Matthew-Wood syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 01, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;T;T;.;T;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.;M;M;.;M;.;.;.
MutationTaster
Benign
D;D;D;N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;.;.;.;D;.;.
REVEL
Pathogenic
Sift
Uncertain
D;D;D;.;.;.;D;.;.
Sift4G
Uncertain
D;D;D;D;D;D;D;D;D
Polyphen
D;D;D;D;.;D;.;D;.
Vest4
MVP
MPC
0.55
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at