chr3-46368646-A-C

Variant names:

• chr3-46368646-A-C
• rs41490645
• ENST00000451485.3:n.572+2598T>G

Variant summary

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

The ENST00000451485.3(CCR5AS):​n.572+2598T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0959 in 152,242 control chromosomes in the GnomAD database, including 956 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 0.096 (956 hom., cov: 32)
• Consequence: CCR5AS ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 10 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR5AS	NR_125406.2	MANE Select	n.572+2598T>G		intron	N/A
	CCR5AS	NR_185891.1		n.344+2598T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR5AS	ENST00000451485.3	TSL:3 MANE Select	n.572+2598T>G		intron	N/A
	CCR5AS	ENST00000701879.2		n.462+2598T>G		intron	N/A
	CCR5AS	ENST00000717843.1		n.325-1362T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14587 AN: 152124 Hom.: 956 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.0780

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0729

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

GnomAD4 genome AF: 0.0959 AC: 14593 AN: 152242 Hom.: 956 Cov.: 32 AF XY: 0.0934 AC XY: 6950 AN XY: 74434

African (AFR) AF: 0.0275 AC: 1144 AN: 41548

American (AMR) AF: 0.0781 AC: 1195 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3468

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

South Asian (SAS) AF: 0.0193 AC: 93 AN: 4830

European-Finnish (FIN) AF: 0.152 AC: 1612 AN: 10588

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

European-Non Finnish (NFE) AF: 0.142 AC: 9658 AN: 68008

Other (OTH) AF: 0.0721 AC: 152 AN: 2108

Alfa AF: 0.119 Hom.: 167

Bravo AF: 0.0883

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs41490645; hg19: chr3-46410137;