rs3087253

Variant names:

• chr3-46377198-C-T
• rs3087253
• ENST00000451485.3:n.399-5781G>A

Variant summary

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

The ENST00000451485.3(CCR5AS):​n.399-5781G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,062 control chromosomes in the GnomAD database, including 30,847 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 0.63 (30847 hom., cov: 32)
• Consequence: CCR5AS ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24
• Publications: 13 publications found

Genes affected

CCR5AS (HGNC:54398): (CCR5 antisense RNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451485.3. 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
	CCR5AS	NR_125406.2	MANE Select	n.399-5781G>A		intron	N/A
	CCR5AS	NR_185891.1		n.171-5781G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR5AS	ENST00000451485.3	TSL:3 MANE Select	n.399-5781G>A		intron	N/A
	CCR5AS	ENST00000701879.2		n.289-5781G>A		intron	N/A
	CCR5AS	ENST00000717843.1		n.151-5781G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95162 AN: 151944 Hom.: 30799 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.626 AC: 95250 AN: 152062 Hom.: 30847 Cov.: 32 AF XY: 0.632 AC XY: 46943 AN XY: 74318

African (AFR) AF: 0.774 AC: 32102 AN: 41482

American (AMR) AF: 0.640 AC: 9790 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1951 AN: 3466

East Asian (EAS) AF: 0.806 AC: 4170 AN: 5174

South Asian (SAS) AF: 0.736 AC: 3554 AN: 4826

European-Finnish (FIN) AF: 0.521 AC: 5500 AN: 10552

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36088 AN: 67960

Other (OTH) AF: 0.630 AC: 1330 AN: 2110

Alfa AF: 0.594 Hom.: 4269

Bravo AF: 0.641

Asia WGS AF: 0.722 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0020
DANN	Benign	0.54
PhyloP100		-3.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3087253;

hg19: chr3-46418689;