8-27690648-A-T

Position:

• chr8-27690648-A-T

Variant summary

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

The XM_017013536.3(SCARA3):​c.1370-7544A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,088 control chromosomes in the GnomAD database, including 9,645 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 0.34 (9645 hom., cov: 32)
• Consequence: SCARA3 XM_017013536.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCARA3	XM_017013536.3	c.1370-7544A>T		intron_variant			XP_016869025.1
SCARA3	XM_017013537.2	c.1370-7544A>T		intron_variant			XP_016869026.1
LOC124901921	XR_007060870.1	n.58-183T>A		intron_variant
SCARA3	XR_949419.3	n.1774-7544A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51664 AN: 151970 Hom.: 9648 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.340 AC: 51675 AN: 152088 Hom.: 9645 Cov.: 32 AF XY: 0.340 AC XY: 25250 AN XY: 74308

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.336

Alfa AF: 0.251 Hom.: 713

Bravo AF: 0.334

Asia WGS AF: 0.409 AC: 1420 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7001584; hg19: chr8-27548165;