rs12675698

chr8-16112071-A-G

Variant summary

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

The NM_138715.3(MSR1):c.1223-1853T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,148 control chromosomes in the GnomAD database, including 1,063 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 0.11 (1063 hom., cov: 32)
• Consequence: MSR1 NM_138715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSR1	NM_138715.3	c.1223-1853T>C		intron_variant		ENST00000262101.10
MSR1	NM_001363744.1	c.1277-1853T>C		intron_variant
MSR1	NM_138716.3	c.1034-1853T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSR1	ENST00000262101.10	c.1223-1853T>C		intron_variant		1	NM_138715.3	P1
MSR1	ENST00000355282.6	c.1034-1853T>C		intron_variant		1
MSR1	ENST00000445506.6	c.1277-1853T>C		intron_variant		1
MSR1	ENST00000350896.3	c.1034-1853T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16273 AN: 152030 Hom.: 1062 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0487

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.107 AC: 16305 AN: 152148 Hom.: 1063 Cov.: 32 AF XY: 0.108 AC XY: 8051 AN XY: 74378

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0487

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0864 Hom.: 75

Bravo AF: 0.114

Asia WGS AF: 0.166 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.65
Dann	Benign	0.57

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: rs12675698; hg19: chr8-15969580;