rs576256

Variant names:

• chr8-27646572-A-G
• rs576256
• NM_016240.3:c.8-3130A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SCARA3	NM_016240.3	c.8-3130A>G		intron_variant	Intron 1 of 5	ENST00000301904.4	NP_057324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARA3	ENST00000301904.4	c.8-3130A>G		intron_variant	Intron 1 of 5	1	NM_016240.3	ENSP00000301904.3
SCARA3	ENST00000337221.8	c.8-3130A>G		intron_variant	Intron 1 of 5	1		ENSP00000337985.3

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

African (AFR) AF: 0.0801 AC: 3327 AN: 41536

American (AMR) AF: 0.231 AC: 3530 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3468

East Asian (EAS) AF: 0.181 AC: 934 AN: 5154

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4820

European-Finnish (FIN) AF: 0.201 AC: 2128 AN: 10604

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16111 AN: 67980

Other (OTH) AF: 0.217 AC: 458 AN: 2114

Alfa AF: 0.198 Hom.: 435

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
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs576256; hg19: chr8-27504089;