chr8-27662667-G-A

Variant names:

• chr8-27662667-G-A
• rs492786
• NM_016240.3:c.1369+3128G>A

Variant summary

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

The NM_016240.3(SCARA3):​c.1369+3128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,132 control chromosomes in the GnomAD database, including 10,517 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 0.35 (10517 hom., cov: 33)
• Consequence: SCARA3 NM_016240.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 3 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=-0.61).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016240.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCARA3	NM_016240.3	MANE Select	c.1369+3128G>A		intron	N/A	NP_057324.2
	SCARA3	NM_182826.2		c.1369+3128G>A		intron	N/A	NP_878185.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCARA3	ENST00000301904.4	TSL:1 MANE Select	c.1369+3128G>A		intron	N/A	ENSP00000301904.3
	SCARA3	ENST00000337221.8	TSL:1	c.1369+3128G>A		intron	N/A	ENSP00000337985.3

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53329 AN: 152014 Hom.: 10516 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.351 AC: 53343 AN: 152132 Hom.: 10517 Cov.: 33 AF XY: 0.352 AC XY: 26197 AN XY: 74368

African (AFR) AF: 0.161 AC: 6684 AN: 41518

American (AMR) AF: 0.419 AC: 6404 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1683 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2427 AN: 5170

South Asian (SAS) AF: 0.522 AC: 2517 AN: 4824

European-Finnish (FIN) AF: 0.345 AC: 3642 AN: 10568

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28583 AN: 67974

Other (OTH) AF: 0.400 AC: 845 AN: 2112

Alfa AF: 0.406 Hom.: 6662

Bravo AF: 0.348

Asia WGS AF: 0.485 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	12
DANN	Benign	0.94
PhyloP100		0.23
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: rs492786; hg19: chr8-27520184;