rs2439497

Positions:

• chr8-27693205-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017013536.3(SCARA3):​c.1370-4987C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,810 control chromosomes in the GnomAD database, including 2,891 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 0.18 (2891 hom., cov: 32)
• Consequence: SCARA3 XM_017013536.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCARA3	XM_017013536.3	c.1370-4987C>T		intron_variant			XP_016869025.1
SCARA3	XM_017013537.2	c.1370-4987C>T		intron_variant			XP_016869026.1
		n.27693205C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26589 AN: 151702 Hom.: 2894 Cov.: 32

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.215

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.175 AC: 26585 AN: 151810 Hom.: 2891 Cov.: 32 AF XY: 0.177 AC XY: 13085 AN XY: 74126

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.215

Alfa AF: 0.226 Hom.: 1750

Bravo AF: 0.170

Asia WGS AF: 0.205 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	3.7
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2439497; hg19: chr8-27550722;