XM_017013536.3:c.1370-16339T>C

Variant names:

• chr8-27681853-T-C
• rs559251
• XM_017013536.3:c.1370-16339T>C

Variant summary

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

The XM_017013536.3(SCARA3):​c.1370-16339T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,122 control chromosomes in the GnomAD database, including 27,948 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 0.59 (27948 hom., cov: 33)
• Consequence: SCARA3 XM_017013536.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

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 (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARA3	XM_017013536.3	c.1370-16339T>C		intron_variant	Intron 5 of 6		XP_016869025.1
SCARA3	XM_017013537.2	c.1370-16339T>C		intron_variant	Intron 5 of 6		XP_016869026.1
SCARA3	XR_949419.3	n.1773+5180T>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90350 AN: 152006 Hom.: 27954 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.594 AC: 90383 AN: 152122 Hom.: 27948 Cov.: 33 AF XY: 0.595 AC XY: 44237 AN XY: 74362

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.590

Alfa AF: 0.663 Hom.: 56256

Bravo AF: 0.578

Asia WGS AF: 0.507 AC: 1764 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	0.64
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs559251; hg19: chr8-27539370;