8-27725308-T-C

Position:

• chr8-27725308-T-C

Variant summary

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

The XM_017013536.3(SCARA3):​c.1418-8048T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,614 control chromosomes in the GnomAD database, including 13,884 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 0.42 (13884 hom., cov: 31)
• Consequence: SCARA3 XM_017013536.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCARA3	XM_017013536.3	c.1418-8048T>C		intron_variant			XP_016869025.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64047 AN: 151510 Hom.: 13858 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.423 AC: 64126 AN: 151614 Hom.: 13884 Cov.: 31 AF XY: 0.423 AC XY: 31331 AN XY: 74056

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.408

Alfa AF: 0.440 Hom.: 2332

Bravo AF: 0.433

Asia WGS AF: 0.548 AC: 1901 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4352802; hg19: chr8-27582825;