rs9859136

Variant names:

• chr3-46053778-G-A
• rs9859136
• NM_001381860.1:c.-32+142C>T

Variant summary

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

The NM_001381860.1(XCR1):​c.-32+142C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,944 control chromosomes in the GnomAD database, including 2,415 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 0.12 (2415 hom., cov: 31)
• Consequence: XCR1 NM_001381860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 2 publications found

Genes affected

XCR1 (HGNC:1625): (X-C motif chemokine receptor 1) The protein encoded by this gene is a chemokine receptor belonging to the G protein-coupled receptor superfamily. The family members are characterized by the presence of 7 transmembrane domains. The encoded protein transduces a signal by increasing the intracellular calcium ion level. The viral macrophage inflammatory protein-II is an antagonist of this receptor and blocks signaling. Some studies have implicated a cluster of genes at 3p21.31, including this gene, as associated with COVID-19 risk. The encoded protein may also play a role in cell proliferation and migration in several types of cancer. [provided by RefSeq, Jan 2023]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XCR1	NM_001381860.1	c.-32+142C>T		intron_variant	Intron 3 of 3		NP_001368789.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XCR1	ENST00000683768.1	c.-32+142C>T		intron_variant	Intron 5 of 5			ENSP00000507745.1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17757 AN: 151826 Hom.: 2410 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0505

Gnomad ASJ AF: 0.00808

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00884

Gnomad FIN AF: 0.0439

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.117 AC: 17785 AN: 151944 Hom.: 2415 Cov.: 31 AF XY: 0.112 AC XY: 8347 AN XY: 74268

African (AFR) AF: 0.333 AC: 13792 AN: 41414

American (AMR) AF: 0.0504 AC: 770 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00808 AC: 28 AN: 3464

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.00885 AC: 42 AN: 4746

European-Finnish (FIN) AF: 0.0439 AC: 465 AN: 10582

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0366 AC: 2490 AN: 67972

Other (OTH) AF: 0.0808 AC: 170 AN: 2104

Alfa AF: 0.0866 Hom.: 200

Bravo AF: 0.130

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.18
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs9859136; hg19: chr3-46095270;