rs11778402

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.08
Variant links:
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]

Genome browser will be placed here

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
SCARA3XM_017013536.3 linkuse as main transcriptc.1370-4075T>A intron_variant XP_016869025.1
SCARA3XM_017013537.2 linkuse as main transcriptc.1370-4075T>A intron_variant XP_016869026.1
use as main transcriptn.27694117T>A intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.427
AC:
64964
AN:
151978
Hom.:
15058
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.242
Gnomad AMI
AF:
0.531
Gnomad AMR
AF:
0.451
Gnomad ASJ
AF:
0.352
Gnomad EAS
AF:
0.457
Gnomad SAS
AF:
0.415
Gnomad FIN
AF:
0.506
Gnomad MID
AF:
0.383
Gnomad NFE
AF:
0.524
Gnomad OTH
AF:
0.415
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.427
AC:
64976
AN:
152098
Hom.:
15055
Cov.:
32
AF XY:
0.428
AC XY:
31858
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.242
Gnomad4 AMR
AF:
0.451
Gnomad4 ASJ
AF:
0.352
Gnomad4 EAS
AF:
0.456
Gnomad4 SAS
AF:
0.415
Gnomad4 FIN
AF:
0.506
Gnomad4 NFE
AF:
0.524
Gnomad4 OTH
AF:
0.417
Alfa
AF:
0.472
Hom.:
2270
Bravo
AF:
0.413
Asia WGS
AF:
0.442
AC:
1536
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
10
DANN
Benign
0.69

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11778402; hg19: chr8-27551634; API