NM_138715.3:c.979+345T>G

Variant names:

• chr8-16149886-A-C
• rs351554
• NM_138715.3:c.979+345T>G

Variant summary

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

The NM_138715.3(MSR1):​c.979+345T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,122 control chromosomes in the GnomAD database, including 9,041 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 0.28 (9041 hom., cov: 29)
• Consequence: MSR1 NM_138715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 5 publications found

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]

MSR1 Gene-Disease associations (from GenCC):

• Barrett esophagus

  Inheritance: Unknown Classification: LIMITED Submitted by: Laboratory for Molecular Medicine

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138715.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSR1	NM_138715.3	MANE Select	c.979+345T>G		intron	N/A	NP_619729.1
	MSR1	NM_001363744.1		c.1033+345T>G		intron	N/A	NP_001350673.1
	MSR1	NM_138716.3		c.979+345T>G		intron	N/A	NP_619730.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSR1	ENST00000262101.10	TSL:1 MANE Select	c.979+345T>G		intron	N/A	ENSP00000262101.5
	MSR1	ENST00000445506.6	TSL:1	c.1033+345T>G		intron	N/A	ENSP00000405453.2
	MSR1	ENST00000355282.6	TSL:1	c.979+345T>G		intron	N/A	ENSP00000347430.2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42758 AN: 151008 Hom.: 9003 Cov.: 29

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.0958

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.284 AC: 42859 AN: 151122 Hom.: 9041 Cov.: 29 AF XY: 0.287 AC XY: 21172 AN XY: 73802

African (AFR) AF: 0.548 AC: 22515 AN: 41104

American (AMR) AF: 0.380 AC: 5746 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3464

East Asian (EAS) AF: 0.546 AC: 2792 AN: 5110

South Asian (SAS) AF: 0.320 AC: 1526 AN: 4770

European-Finnish (FIN) AF: 0.0730 AC: 762 AN: 10442

Middle Eastern (MID) AF: 0.240 AC: 69 AN: 288

European-Non Finnish (NFE) AF: 0.121 AC: 8177 AN: 67832

Other (OTH) AF: 0.274 AC: 574 AN: 2094

Alfa AF: 0.179 Hom.: 6248

Bravo AF: 0.322

Asia WGS AF: 0.423 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.65
PhyloP100		0.047
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: rs351554; hg19: chr8-16007395;