rs3824098

Variant names:

• chr8-27665113-A-C
• rs3824098
• NM_016240.3:c.1369+5574A>C

Your query was ambiguous. Multiple possible variants found:

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

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+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
• Publications: 2 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=-0.89).
• 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 rank	MANE	Protein	UniProt
SCARA3	NM_016240.3	c.1369+5574A>C		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+5574A>C		intron_variant	Intron 5 of 5	1	NM_016240.3	ENSP00000301904.3
SCARA3	ENST00000337221.8	c.1369+5574A>C		intron_variant	Intron 5 of 5	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

African (AFR) AF: 0.0740 AC: 3074 AN: 41560

American (AMR) AF: 0.120 AC: 1829 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1397 AN: 5164

South Asian (SAS) AF: 0.160 AC: 770 AN: 4824

European-Finnish (FIN) AF: 0.0752 AC: 798 AN: 10608

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7014 AN: 68002

Other (OTH) AF: 0.123 AC: 259 AN: 2112

Alfa AF: 0.0218 Hom.: 13

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
PhyloP100		-0.068
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: rs3824098; hg19: chr8-27522630;