rs576256

chr8-27646572-A-G

Variant summary

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

The NM_016240.3(SCARA3):c.8-3130A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,182 control chromosomes in the GnomAD database, including 3,290 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 0.19 (3290 hom., cov: 32)
• Consequence: SCARA3 NM_016240.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCARA3	NM_016240.3	c.8-3130A>G		intron_variant		ENST00000301904.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCARA3	ENST00000301904.4	c.8-3130A>G		intron_variant		1	NM_016240.3	P1
SCARA3	ENST00000337221.8	c.8-3130A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29294 AN: 152064 Hom.: 3290 Cov.: 32

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.193 AC: 29310 AN: 152182 Hom.: 3290 Cov.: 32 AF XY: 0.194 AC XY: 14439 AN XY: 74404

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.217

Alfa AF: 0.202 Hom.: 432

Bravo AF: 0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.34
Dann	Benign	0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs576256; hg19: chr8-27504089;