rs17141079

Variant names:

• chr3-46383078-A-T
• rs17141079
• ENST00000451485.3:n.398+9747T>A

Variant summary

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

The ENST00000451485.3(CCR5AS):​n.398+9747T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,106 control chromosomes in the GnomAD database, including 9,655 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 0.32 (9655 hom., cov: 32)
• Consequence: CCR5AS ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 8 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 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+9747T>A		intron	N/A
	CCR5AS	NR_185891.1		n.171-11661T>A		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+9747T>A		intron	N/A
	CCR5AS	ENST00000701879.2		n.289-11661T>A		intron	N/A
	CCR5AS	ENST00000717843.1		n.151-11661T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48450 AN: 151986 Hom.: 9633 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.319 AC: 48522 AN: 152106 Hom.: 9655 Cov.: 32 AF XY: 0.316 AC XY: 23460 AN XY: 74348

African (AFR) AF: 0.563 AC: 23347 AN: 41484

American (AMR) AF: 0.181 AC: 2774 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3468

East Asian (EAS) AF: 0.0343 AC: 178 AN: 5184

South Asian (SAS) AF: 0.224 AC: 1082 AN: 4828

European-Finnish (FIN) AF: 0.306 AC: 3235 AN: 10570

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16101 AN: 67968

Other (OTH) AF: 0.252 AC: 533 AN: 2114

Alfa AF: 0.291 Hom.: 950

Bravo AF: 0.321

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.50
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs17141079; hg19: chr3-46424569;