rs1526427

Positions:

• chr8-16552983-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061175.1(LOC101929028):​n.873-41073A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0534 in 152,112 control chromosomes in the GnomAD database, including 706 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 0.053 (706 hom., cov: 31)
• Consequence: LOC101929028 XR_007061175.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

LOC101929028 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929028	XR_007061175.1	n.873-41073A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSR1	ENST00000518026.5	c.-244+14267A>G		intron_variant		4
MSR1	ENST00000518343.5	n.29+14409A>G		intron_variant, non_coding_transcript_variant		4
MSR1	ENST00000522130.1	n.152+12552A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0534 AC: 8115 AN: 151992 Hom.: 700 Cov.: 31

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.00895

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0534 AC: 8128 AN: 152112 Hom.: 706 Cov.: 31 AF XY: 0.0589 AC XY: 4383 AN XY: 74362

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0285

Gnomad4 NFE AF: 0.0115

Gnomad4 OTH AF: 0.0558

Alfa AF: 0.0208 Hom.: 147

Bravo AF: 0.0642

Asia WGS AF: 0.220 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1526427; hg19: chr8-16410492;