rs492786

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-27662667-G-A
• chr8-27662667-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.61).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARA3	NM_016240.3	c.1369+3128G>A		intron_variant	Intron 5 of 5	ENST00000301904.4	NP_057324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARA3	ENST00000301904.4	c.1369+3128G>A		intron_variant	Intron 5 of 5	1	NM_016240.3	ENSP00000301904.3
SCARA3	ENST00000337221.8	c.1369+3128G>A		intron_variant	Intron 5 of 5	1		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

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.400

Alfa AF: 0.409 Hom.: 5983

Bravo AF: 0.348

Asia WGS AF: 0.485 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	12
DANN	Benign	0.94

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

Publications

LitVar

Other links and lift over

dbSNP: rs492786; hg19: chr8-27520184;