rs3087253

chr3-46377198-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125406.1(CCR5AS):n.392-5781G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,062 control chromosomes in the GnomAD database, including 30,847 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 0.63 (30847 hom., cov: 32)
• Consequence: CCR5AS NR_125406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24

Genes affected

CCR5AS (HGNC:54398): (CCR5 antisense RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR5AS	NR_125406.1	n.392-5781G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR5AS	ENST00000701879.1	n.174-5781G>A		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.392-5781G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95162 AN: 151944 Hom.: 30799 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.626 AC: 95250 AN: 152062 Hom.: 30847 Cov.: 32 AF XY: 0.632 AC XY: 46943 AN XY: 74318

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.630

Alfa AF: 0.594 Hom.: 4269

Bravo AF: 0.641

Asia WGS AF: 0.722 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.0020
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3087253; hg19: chr3-46418689;