rs10503575

chr8-16124370-C-T

Variant summary

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

The NM_138715.3(MSR1):c.1034-3764G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,130 control chromosomes in the GnomAD database, including 41,446 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 0.70 (41446 hom., cov: 33)
• Consequence: MSR1 NM_138715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

Genes affected

MSR1 (HGNC:7376): (macrophage scavenger receptor 1) This gene encodes the class A macrophage scavenger receptors, which include three different types (1, 2, 3) generated by alternative splicing of this gene. These receptors or isoforms are macrophage-specific trimeric integral membrane glycoproteins and have been implicated in many macrophage-associated physiological and pathological processes including atherosclerosis, Alzheimer's disease, and host defense. The isoforms type 1 and type 2 are functional receptors and are able to mediate the endocytosis of modified low density lipoproteins (LDLs). The isoform type 3 does not internalize modified LDL (acetyl-LDL) despite having the domain shown to mediate this function in the types 1 and 2 isoforms. It has an altered intracellular processing and is trapped within the endoplasmic reticulum, making it unable to perform endocytosis. The isoform type 3 can inhibit the function of isoforms type 1 and type 2 when co-expressed, indicating a dominant negative effect and suggesting a mechanism for regulation of scavenger receptor activity in macrophages. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSR1	NM_138715.3	c.1034-3764G>A		intron_variant		ENST00000262101.10
MSR1	NM_001363744.1	c.1088-3764G>A		intron_variant
MSR1	NM_138716.3	c.1034-14152G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSR1	ENST00000262101.10	c.1034-3764G>A		intron_variant		1	NM_138715.3	P1

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105890 AN: 152014 Hom.: 41438 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.696 AC: 105907 AN: 152130 Hom.: 41446 Cov.: 33 AF XY: 0.700 AC XY: 52071 AN XY: 74370

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.748

Alfa AF: 0.842 Hom.: 78274

Bravo AF: 0.663

Asia WGS AF: 0.730 AC: 2538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.4
Dann	Benign	0.81

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503575; hg19: chr8-15981879;