chr8-27690648-A-T

Variant names:

• chr8-27690648-A-T
• rs7001584
• XM_017013536.3:c.1370-7544A>T

Variant summary

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

The XR_949419.3(SCARA3):​n.1774-7544A>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 XR_949419.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.187 AC: 7769 AN: 41518

American (AMR) AF: 0.389 AC: 5945 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 796 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2348 AN: 5154

South Asian (SAS) AF: 0.339 AC: 1634 AN: 4826

European-Finnish (FIN) AF: 0.367 AC: 3877 AN: 10560

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28127 AN: 67960

Other (OTH) AF: 0.336 AC: 710 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.31
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs7001584; hg19: chr8-27548165;