rs11778402

Variant names:

• chr8-27694117-T-A
• rs11778402
• XM_017013536.3:c.1370-4075T>A

Variant summary

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

The XM_017013536.3(SCARA3):​c.1370-4075T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,098 control chromosomes in the GnomAD database, including 15,055 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 0.43 (15055 hom., cov: 32)
• Consequence: SCARA3 XM_017013536.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08
• 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]

LOC124901921 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARA3	XM_017013536.3	c.1370-4075T>A		intron_variant	Intron 5 of 6		XP_016869025.1
SCARA3	XM_017013537.2	c.1370-4075T>A		intron_variant	Intron 5 of 6		XP_016869026.1
LOC124901921	XR_007060870.1	n.57+16A>T		intron_variant	Intron 1 of 2
SCARA3	XR_949419.3	n.1774-4075T>A		intron_variant	Intron 6 of 6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64964 AN: 151978 Hom.: 15058 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.427 AC: 64976 AN: 152098 Hom.: 15055 Cov.: 32 AF XY: 0.428 AC XY: 31858 AN XY: 74370

African (AFR) AF: 0.242 AC: 10060 AN: 41518

American (AMR) AF: 0.451 AC: 6888 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2359 AN: 5170

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4818

European-Finnish (FIN) AF: 0.506 AC: 5365 AN: 10594

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35613 AN: 67938

Other (OTH) AF: 0.417 AC: 879 AN: 2106

Alfa AF: 0.472 Hom.: 2270

Bravo AF: 0.413

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.69
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs11778402; hg19: chr8-27551634;