rs3824098

Positions:

• chr8-27665113-A-C
• chr8-27665113-A-T

Variant summary

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

The NM_016240.3(SCARA3):​c.1369+5574A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,240 control chromosomes in the GnomAD database, including 949 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 0.10 (949 hom., cov: 33)
• Consequence: SCARA3 NM_016240.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCARA3	NM_016240.3	c.1369+5574A>C		intron_variant		ENST00000301904.4	NP_057324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCARA3	ENST00000301904.4	c.1369+5574A>C		intron_variant		1	NM_016240.3	ENSP00000301904.3
SCARA3	ENST00000337221.8	c.1369+5574A>C		intron_variant		1		ENSP00000337985.3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15860 AN: 152122 Hom.: 950 Cov.: 33

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.104 AC: 15861 AN: 152240 Hom.: 949 Cov.: 33 AF XY: 0.105 AC XY: 7803 AN XY: 74430

Gnomad4 AFR AF: 0.0740

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0752

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0200 Hom.: 12

Bravo AF: 0.107

Asia WGS AF: 0.206 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.56

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: rs3824098; hg19: chr8-27522630;