rs17467992

Variant names:

• chr8-27639164-C-A
• rs17467992
• NM_016240.3:c.7+4957C>A

Variant summary

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

The NM_016240.3(SCARA3):​c.7+4957C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,986 control chromosomes in the GnomAD database, including 10,461 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 0.33 (10461 hom., cov: 31)
• Consequence: SCARA3 NM_016240.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARA3	NM_016240.3	c.7+4957C>A		intron_variant	Intron 1 of 5	ENST00000301904.4	NP_057324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARA3	ENST00000301904.4	c.7+4957C>A		intron_variant	Intron 1 of 5	1	NM_016240.3	ENSP00000301904.3
SCARA3	ENST00000337221.8	c.7+4957C>A		intron_variant	Intron 1 of 5	1		ENSP00000337985.3

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50111 AN: 151868 Hom.: 10461 Cov.: 31

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.330 AC: 50111 AN: 151986 Hom.: 10461 Cov.: 31 AF XY: 0.330 AC XY: 24513 AN XY: 74278

African (AFR) AF: 0.0856 AC: 3551 AN: 41472

American (AMR) AF: 0.343 AC: 5248 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1497 AN: 3470

East Asian (EAS) AF: 0.163 AC: 844 AN: 5174

South Asian (SAS) AF: 0.303 AC: 1460 AN: 4814

European-Finnish (FIN) AF: 0.477 AC: 5025 AN: 10526

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

European-Non Finnish (NFE) AF: 0.461 AC: 31327 AN: 67940

Other (OTH) AF: 0.337 AC: 707 AN: 2100

Alfa AF: 0.404 Hom.: 1757

Bravo AF: 0.307

Asia WGS AF: 0.247 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		0.13
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: rs17467992; hg19: chr8-27496681;