rs916093

Variant names:

• chr3-46403303-T-C
• rs916093
• ENST00000451485.3:n.170+3594A>G

Variant summary

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

The ENST00000451485.3(CCR5AS):​n.170+3594A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,160 control chromosomes in the GnomAD database, including 3,356 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 0.19 (3356 hom., cov: 32)
• Consequence: CCR5AS ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR5AS	NR_125406.2	n.170+3594A>G		intron_variant	Intron 1 of 3
CCR5AS	NR_185891.1	n.170+3594A>G		intron_variant	Intron 1 of 2
CCR5AS	NR_185892.1	n.170+3594A>G		intron_variant	Intron 1 of 2
CCR5AS	NR_185893.1	n.170+3594A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR5AS	ENST00000451485.3	n.170+3594A>G		intron_variant	Intron 1 of 3	3
CCR5AS	ENST00000686150.3	n.226+3594A>G		intron_variant	Intron 1 of 2
CCR5AS	ENST00000691693.3	n.239+3594A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28138 AN: 152042 Hom.: 3345 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.185 AC: 28186 AN: 152160 Hom.: 3356 Cov.: 32 AF XY: 0.179 AC XY: 13310 AN XY: 74396

African (AFR) AF: 0.330 AC: 13693 AN: 41472

American (AMR) AF: 0.114 AC: 1744 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0216 AC: 104 AN: 4824

European-Finnish (FIN) AF: 0.152 AC: 1615 AN: 10594

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10004 AN: 68006

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.193 Hom.: 514

Bravo AF: 0.191

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.63
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs916093; hg19: chr3-46444794;