8-16143708-T-TATA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_138715.3(MSR1):​c.980-98_980-97insTAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 828,288 control chromosomes in the GnomAD database, including 9,870 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 2543 hom., cov: 30)
Exomes 𝑓: 0.10 ( 7327 hom. )

Consequence

MSR1
NM_138715.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0580
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MSR1NM_138715.3 linkc.980-98_980-97insTAT intron_variant ENST00000262101.10 NP_619729.1 P21757-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MSR1ENST00000262101.10 linkc.980-98_980-97insTAT intron_variant 1 NM_138715.3 ENSP00000262101.5 P21757-1

Frequencies

GnomAD3 genomes
AF:
0.142
AC:
21558
AN:
151840
Hom.:
2530
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.273
Gnomad AMI
AF:
0.0252
Gnomad AMR
AF:
0.170
Gnomad ASJ
AF:
0.0674
Gnomad EAS
AF:
0.443
Gnomad SAS
AF:
0.204
Gnomad FIN
AF:
0.0284
Gnomad MID
AF:
0.0791
Gnomad NFE
AF:
0.0529
Gnomad OTH
AF:
0.126
GnomAD4 exome
AF:
0.101
AC:
68213
AN:
676330
Hom.:
7327
AF XY:
0.102
AC XY:
36985
AN XY:
361144
show subpopulations
Gnomad4 AFR exome
AF:
0.270
Gnomad4 AMR exome
AF:
0.223
Gnomad4 ASJ exome
AF:
0.0582
Gnomad4 EAS exome
AF:
0.464
Gnomad4 SAS exome
AF:
0.177
Gnomad4 FIN exome
AF:
0.0258
Gnomad4 NFE exome
AF:
0.0523
Gnomad4 OTH exome
AF:
0.105
GnomAD4 genome
AF:
0.142
AC:
21612
AN:
151958
Hom.:
2543
Cov.:
30
AF XY:
0.145
AC XY:
10744
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.274
Gnomad4 AMR
AF:
0.170
Gnomad4 ASJ
AF:
0.0674
Gnomad4 EAS
AF:
0.443
Gnomad4 SAS
AF:
0.204
Gnomad4 FIN
AF:
0.0284
Gnomad4 NFE
AF:
0.0529
Gnomad4 OTH
AF:
0.128
Alfa
AF:
0.0981
Hom.:
165
Bravo
AF:
0.161
Asia WGS
AF:
0.282
AC:
976
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3036811; hg19: chr8-16001217; API