chr8-16120616-T-TAAA

Variant names:

• chr8-16120616-T-TAAA
• rs60866666
• NM_138715.3:c.1034-13_1034-11dupTTT

Variant summary

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

The NM_138715.3(MSR1):​c.1034-13_1034-11dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0042 (3 hom., cov: 0)
  • Exomes 𝑓: 0.0080 (6 hom.)
• Consequence: MSR1 NM_138715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• 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 = 0.00417 (265/63482) while in subpopulation AFR AF = 0.0145 (238/16448). AF 95% confidence interval is 0.013. There are 3 homozygotes in GnomAd4. There are 128 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 3 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.1034-13_1034-11dupTTT		intron	N/A	NP_619729.1	P21757-1
	MSR1	NM_001363744.1		c.1088-13_1088-11dupTTT		intron	N/A	NP_001350673.1	B4DDJ5
	MSR1	NM_138716.3		c.1034-10401_1034-10399dupTTT		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.1034-11_1034-10insTTT		intron	N/A	ENSP00000262101.5	P21757-1
	MSR1	ENST00000445506.6	TSL:1	c.1088-11_1088-10insTTT		intron	N/A	ENSP00000405453.2	B4DDJ5
	MSR1	ENST00000355282.6	TSL:1	c.1034-10399_1034-10398insTTT		intron	N/A	ENSP00000347430.2	P21757-3

Frequencies

GnomAD3 genomes AF: 0.00416 AC: 264 AN: 63480 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00216

Gnomad ASJ AF: 0.000504

Gnomad EAS AF: 0.00240

Gnomad SAS AF: 0.000664

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000285

Gnomad OTH AF: 0.00131

GnomAD4 exome AF: 0.00798 AC: 8954 AN: 1122508 Hom.: 6 Cov.: 0 AF XY: 0.00793 AC XY: 4406 AN XY: 555870

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

African (AFR) AF: 0.0206 AC: 453 AN: 21954

American (AMR) AF: 0.0208 AC: 458 AN: 22024

Ashkenazi Jewish (ASJ) AF: 0.00747 AC: 145 AN: 19422

East Asian (EAS) AF: 0.0217 AC: 592 AN: 27220

South Asian (SAS) AF: 0.00482 AC: 290 AN: 60168

European-Finnish (FIN) AF: 0.00874 AC: 228 AN: 26078

Middle Eastern (MID) AF: 0.00856 AC: 26 AN: 3036

European-Non Finnish (NFE) AF: 0.00708 AC: 6349 AN: 897120

Other (OTH) AF: 0.00908 AC: 413 AN: 45486

⚠️ 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: 0.00417 AC: 265 AN: 63482 Hom.: 3 Cov.: 0 AF XY: 0.00448 AC XY: 128 AN XY: 28554

African (AFR) AF: 0.0145 AC: 238 AN: 16448

American (AMR) AF: 0.00216 AC: 9 AN: 4160

Ashkenazi Jewish (ASJ) AF: 0.000504 AC: 1 AN: 1986

East Asian (EAS) AF: 0.00240 AC: 5 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: 0.000285 AC: 10 AN: 35062

Other (OTH) AF: 0.00131 AC: 1 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		0.14
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs60866666; hg19: chr8-15978125;