rs11575815

Variant names:

• chr3-46378679-A-T
• rs11575815
• ENST00000451485.3:n.399-7262T>A

Variant summary

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

The ENST00000451485.3(CCR5AS):​n.399-7262T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,076 control chromosomes in the GnomAD database, including 7,858 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 0.30 (7858 hom., cov: 32)
• Consequence: CCR5AS ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR5AS	NR_125406.2	n.399-7262T>A		intron_variant	Intron 2 of 3
CCR5AS	NR_185891.1	n.171-7262T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR5AS	ENST00000451485.3	n.399-7262T>A		intron_variant	Intron 2 of 3	3
CCR5AS	ENST00000701879.2	n.289-7262T>A		intron_variant	Intron 1 of 2
CCR5AS	ENST00000717843.1	n.151-7262T>A		intron_variant	Intron 1 of 3
CCR5AS	ENST00000717851.1	n.230-1790T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45790 AN: 151960 Hom.: 7859 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.301 AC: 45792 AN: 152076 Hom.: 7858 Cov.: 32 AF XY: 0.305 AC XY: 22662 AN XY: 74340

African (AFR) AF: 0.127 AC: 5251 AN: 41506

American (AMR) AF: 0.378 AC: 5766 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1327 AN: 3470

East Asian (EAS) AF: 0.558 AC: 2882 AN: 5162

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4814

European-Finnish (FIN) AF: 0.307 AC: 3243 AN: 10550

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24161 AN: 67998

Other (OTH) AF: 0.347 AC: 731 AN: 2106

Alfa AF: 0.302 Hom.: 941

Bravo AF: 0.298

Asia WGS AF: 0.419 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.67
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs11575815; hg19: chr3-46420170;