rs11778402

Positions:

• chr8-27694117-T-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08

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=-0.78).
• 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
SCARA3	XM_017013536.3	c.1370-4075T>A		intron_variant			XP_016869025.1
SCARA3	XM_017013537.2	c.1370-4075T>A		intron_variant			XP_016869026.1
		n.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

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

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

Other links and lift over

dbSNP: rs11778402; hg19: chr8-27551634;