8-16120616-TAAAAAAAAAAAAAAAA-TAAAAAAAAAAAA

Variant names:

• chr8-16120616-TAAAA-T
• rs60866666
• NM_138715.3:c.1034-14_1034-11delTTTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_138715.3(MSR1):​c.1034-14_1034-11delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0494 in 1,156,570 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0032 (2 hom., cov: 0)
  • Exomes 𝑓: 0.052 (0 hom.)
• Consequence: MSR1 NM_138715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 0 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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0032 (203/63500) while in subpopulation AFR AF = 0.00935 (154/16464). AF 95% confidence interval is 0.00815. There are 2 homozygotes in GnomAd4. There are 94 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 2 Unknown gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSR1	NM_138715.3	MANE Select	c.1034-14_1034-11delTTTT		intron	N/A	NP_619729.1	P21757-1
	MSR1	NM_001363744.1		c.1088-14_1088-11delTTTT		intron	N/A	NP_001350673.1	B4DDJ5
	MSR1	NM_138716.3		c.1034-10402_1034-10399delTTTT		intron	N/A	NP_619730.1	P21757-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSR1	ENST00000262101.10	TSL:1 MANE Select	c.1034-14_1034-11delTTTT		intron	N/A	ENSP00000262101.5	P21757-1
	MSR1	ENST00000445506.6	TSL:1	c.1088-14_1088-11delTTTT		intron	N/A	ENSP00000405453.2	B4DDJ5
	MSR1	ENST00000355282.6	TSL:1	c.1034-10402_1034-10399delTTTT		intron	N/A	ENSP00000347430.2	P21757-3

Frequencies

GnomAD3 genomes AF: 0.00320 AC: 203 AN: 63498 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00937

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00144

Gnomad ASJ AF: 0.00706

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000664

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000627

Gnomad OTH AF: 0.00787

GnomAD4 exome AF: 0.0521 AC: 56912 AN: 1093070 Hom.: 0 AF XY: 0.0520 AC XY: 28077 AN XY: 539556

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0496 AC: 1079 AN: 21770

American (AMR) AF: 0.0412 AC: 880 AN: 21354

Ashkenazi Jewish (ASJ) AF: 0.0604 AC: 1133 AN: 18758

East Asian (EAS) AF: 0.0429 AC: 1145 AN: 26704

South Asian (SAS) AF: 0.0330 AC: 1902 AN: 57692

European-Finnish (FIN) AF: 0.0765 AC: 1908 AN: 24956

Middle Eastern (MID) AF: 0.0616 AC: 181 AN: 2936

European-Non Finnish (NFE) AF: 0.0529 AC: 46253 AN: 874598

Other (OTH) AF: 0.0549 AC: 2431 AN: 44302

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.00320 AC: 203 AN: 63500 Hom.: 2 Cov.: 0 AF XY: 0.00329 AC XY: 94 AN XY: 28558

African (AFR) AF: 0.00935 AC: 154 AN: 16464

American (AMR) AF: 0.00144 AC: 6 AN: 4162

Ashkenazi Jewish (ASJ) AF: 0.00706 AC: 14 AN: 1984

East Asian (EAS) AF: 0.00 AC: 0 AN: 2082

South Asian (SAS) AF: 0.000671 AC: 1 AN: 1490

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 938

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 58

European-Non Finnish (NFE) AF: 0.000627 AC: 22 AN: 35064

Other (OTH) AF: 0.00783 AC: 6 AN: 766

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5
Mutation Taster		=100/0	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: rs60866666; hg19: chr8-15978125;