rs757365316

Variant names:

• chr8-27651510-C-G
• rs757365316
• NM_016240.3:c.109C>G

Your query was ambiguous. Multiple possible variants found:

• chr8-27651510-C-G
• chr8-27651510-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_016240.3(SCARA3):​c.109C>G​(p.Arg37Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R37W) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SCARA3 NM_016240.3 missense, splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.23528117).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARA3	NM_016240.3	c.109C>G	p.Arg37Gly	missense_variant, splice_region_variant	Exon 3 of 6	ENST00000301904.4	NP_057324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARA3	ENST00000301904.4	c.109C>G	p.Arg37Gly	missense_variant, splice_region_variant	Exon 3 of 6	1	NM_016240.3	ENSP00000301904.3
SCARA3	ENST00000337221.8	c.109C>G	p.Arg37Gly	missense_variant, splice_region_variant	Exon 3 of 6	1		ENSP00000337985.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Uncertain	0.032	T
BayesDel_noAF	Benign	-0.19
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.065	.;T
Eigen	Benign	-0.25
Eigen_PC	Benign	-0.16
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Benign	0.73	T;T
M_CAP	Uncertain	0.093	D
MetaRNN	Benign	0.24	T;T
MetaSVM	Uncertain	0.15	D
MutationAssessor	Benign	1.5	L;L
PhyloP100		0.41
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-2.0	N;N
REVEL	Benign	0.049
Sift	Uncertain	0.010	D;D
Sift4G	Uncertain	0.041	D;D
Polyphen		0.49	P;B
Vest4		0.40
MutPred		0.36		Gain of ubiquitination at K35 (P = 0.0325);Gain of ubiquitination at K35 (P = 0.0325);
MVP		0.90
MPC		0.27
ClinPred		0.68	D
GERP RS		4.0
Varity_R		0.14
gMVP		0.39
Mutation Taster		=84/16	polymorphism

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: rs757365316; hg19: chr8-27509027;