rs2040388

chr3-46367240-G-Achr3-46367240-G-T

Variant summary

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

The NR_125406.1(CCR5AS):n.566-2195C>T 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 0.644 in 151,796 control chromosomes in the GnomAD database, including 32,442 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 0.64 (32442 hom., cov: 30)
• Consequence: CCR5AS NR_125406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR5AS	NR_125406.1	n.566-2195C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR5AS	ENST00000701879.1	n.348-2195C>T		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.566-2195C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97731 AN: 151680 Hom.: 32400 Cov.: 30

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.644 AC: 97812 AN: 151796 Hom.: 32442 Cov.: 30 AF XY: 0.649 AC XY: 48137 AN XY: 74180

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.649

Alfa AF: 0.421 Hom.: 997

Bravo AF: 0.659

Asia WGS AF: 0.725 AC: 2519 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.027
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2040388; hg19: chr3-46408731;