chr8-27725308-T-C

Variant names:

• chr8-27725308-T-C
• rs4352802
• ENST00000781883.1:n.99+5249T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000781883.1(ENSG00000253875):​n.99+5249T>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: ENSG00000253875 ENST00000781883.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810
• Publications: 5 publications found

Genes affected

ENSG00000253875 (HGNC:):

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=-0.93).
• 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 rank	MANE	Protein	UniProt
SCARA3	XM_017013536.3	c.1418-8048T>C		intron_variant	Intron 6 of 6		XP_016869025.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253875	ENST00000781883.1	n.99+5249T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.391 AC: 16164 AN: 41358

American (AMR) AF: 0.495 AC: 7536 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 942 AN: 3472

East Asian (EAS) AF: 0.627 AC: 3239 AN: 5162

South Asian (SAS) AF: 0.426 AC: 2047 AN: 4800

European-Finnish (FIN) AF: 0.381 AC: 3963 AN: 10406

Middle Eastern (MID) AF: 0.338 AC: 98 AN: 290

European-Non Finnish (NFE) AF: 0.424 AC: 28801 AN: 67888

Other (OTH) AF: 0.408 AC: 855 AN: 2094

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs4352802; hg19: chr8-27582825;