rs11778402
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_017013536.3(SCARA3):c.1370-4075T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,098 control chromosomes in the GnomAD database, including 15,055 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 0.43 ( 15055 hom., cov: 32)
Consequence
SCARA3
XM_017013536.3 intron
XM_017013536.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.08
Genes affected
SCARA3 (HGNC:19000): (scavenger receptor class A member 3) This gene encodes a macrophage scavenger receptor-like protein. This protein has been shown to deplete reactive oxygen species, and thus play an important role in protecting cells from oxidative stress. The expression of this gene is induced by oxidative stress. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCARA3 | XM_017013536.3 | c.1370-4075T>A | intron_variant | XP_016869025.1 | ||||
SCARA3 | XM_017013537.2 | c.1370-4075T>A | intron_variant | XP_016869026.1 | ||||
use as main transcript | n.27694117T>A | intergenic_region |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
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Frequencies
GnomAD3 genomes AF: 0.427 AC: 64964AN: 151978Hom.: 15058 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.427 AC: 64976AN: 152098Hom.: 15055 Cov.: 32 AF XY: 0.428 AC XY: 31858AN XY: 74370
GnomAD4 genome
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31858
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74370
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1536
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at