chr8-16114175-G-A

Variant names:

• chr8-16114175-G-A
• rs1904577
• NM_138715.3:c.1223-3957C>T

Variant summary

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

The NM_138715.3(MSR1):​c.1223-3957C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 151,672 control chromosomes in the GnomAD database, including 43,493 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 0.74 (43493 hom., cov: 29)
• Consequence: MSR1 NM_138715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 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.1223-3957C>T		intron	N/A	NP_619729.1
	MSR1	NM_001363744.1		c.1277-3957C>T		intron	N/A	NP_001350673.1
	MSR1	NM_138716.3		c.1034-3957C>T		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.1223-3957C>T		intron	N/A	ENSP00000262101.5
	MSR1	ENST00000445506.6	TSL:1	c.1277-3957C>T		intron	N/A	ENSP00000405453.2
	MSR1	ENST00000355282.6	TSL:1	c.1034-3957C>T		intron	N/A	ENSP00000347430.2

Frequencies

GnomAD3 genomes AF: 0.738 AC: 111783 AN: 151556 Hom.: 43480 Cov.: 29

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.737 AC: 111816 AN: 151672 Hom.: 43493 Cov.: 29 AF XY: 0.737 AC XY: 54648 AN XY: 74118

African (AFR) AF: 0.468 AC: 19336 AN: 41276

American (AMR) AF: 0.731 AC: 11143 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2889 AN: 3468

East Asian (EAS) AF: 0.747 AC: 3855 AN: 5162

South Asian (SAS) AF: 0.779 AC: 3743 AN: 4804

European-Finnish (FIN) AF: 0.860 AC: 9040 AN: 10506

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.871 AC: 59136 AN: 67916

Other (OTH) AF: 0.763 AC: 1604 AN: 2102

Alfa AF: 0.825 Hom.: 27768

Bravo AF: 0.714

Asia WGS AF: 0.754 AC: 2618 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.23
PhyloP100		0.018
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: rs1904577; hg19: chr8-15971684;