rs2439497

Variant names:

• chr8-27693205-C-T
• rs2439497
• XM_017013536.3:c.1370-4987C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

LOC124901921 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0460 AC: 1905 AN: 41454

American (AMR) AF: 0.216 AC: 3291 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1073 AN: 3466

East Asian (EAS) AF: 0.106 AC: 549 AN: 5166

South Asian (SAS) AF: 0.312 AC: 1496 AN: 4800

European-Finnish (FIN) AF: 0.194 AC: 2019 AN: 10430

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.228 AC: 15460 AN: 67940

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.226 Hom.: 1963

Bravo AF: 0.170

Asia WGS AF: 0.205 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	3.7
DANN	Benign	0.83
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2439497; hg19: chr8-27550722;