chr3-46386699-A-C

Variant names:

• chr3-46386699-A-C
• rs6441975
• ENST00000451485.3:n.398+6126T>G

Variant summary

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

The ENST00000451485.3(CCR5AS):​n.398+6126T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,100 control chromosomes in the GnomAD database, including 44,414 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 0.76 (44414 hom., cov: 32)
• Consequence: CCR5AS ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 14 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 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.398+6126T>G		intron	N/A
	CCR5AS	NR_185891.1		n.171-15282T>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.398+6126T>G		intron	N/A
	CCR5AS	ENST00000701879.2		n.289-15282T>G		intron	N/A
	CCR5AS	ENST00000717843.1		n.151-15282T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115073 AN: 151982 Hom.: 44351 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.757 AC: 115181 AN: 152100 Hom.: 44414 Cov.: 32 AF XY: 0.758 AC XY: 56409 AN XY: 74382

African (AFR) AF: 0.904 AC: 37532 AN: 41502

American (AMR) AF: 0.739 AC: 11293 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2653 AN: 3468

East Asian (EAS) AF: 0.807 AC: 4179 AN: 5180

South Asian (SAS) AF: 0.760 AC: 3664 AN: 4822

European-Finnish (FIN) AF: 0.674 AC: 7134 AN: 10582

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46205 AN: 67954

Other (OTH) AF: 0.737 AC: 1559 AN: 2116

Alfa AF: 0.707 Hom.: 109029

Bravo AF: 0.770

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.60
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs6441975; hg19: chr3-46428190;