rs2640734

chr8-27675137-C-T

Variant summary

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

The ENST00000337221.8(SCARA3):c.1370-1432C>T 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 152,110 control chromosomes in the GnomAD database, including 3,283 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 (3283 hom., cov: 31)
• Consequence: SCARA3 ENST00000337221.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCARA3	NM_182826.2	c.1370-1432C>T		intron_variant
SCARA3	XM_017013536.3	c.1369+15598C>T		intron_variant
SCARA3	XM_017013537.2	c.1369+15598C>T		intron_variant
SCARA3	XR_949419.3	n.1669-1432C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCARA3	ENST00000337221.8	c.1370-1432C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29422 AN: 151992 Hom.: 3288 Cov.: 31

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.193 AC: 29416 AN: 152110 Hom.: 3283 Cov.: 31 AF XY: 0.194 AC XY: 14447 AN XY: 74348

Gnomad4 AFR AF: 0.0833

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.230

Alfa AF: 0.229 Hom.: 2162

Bravo AF: 0.192

Asia WGS AF: 0.213 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.8
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2640734; hg19: chr8-27532654;