rs41490645

Positions:

• chr3-46368646-A-C

Variant summary

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

The NR_125406.1(CCR5AS):​n.565+2598T>G 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 0.0959 in 152,242 control chromosomes in the GnomAD database, including 956 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 0.096 (956 hom., cov: 32)
• Consequence: CCR5AS NR_125406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR5AS	NR_125406.1	n.565+2598T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR5AS	ENST00000701879.1	n.347+2598T>G		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.565+2598T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14587 AN: 152124 Hom.: 956 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.0780

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0729

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

GnomAD4 genome AF: 0.0959 AC: 14593 AN: 152242 Hom.: 956 Cov.: 32 AF XY: 0.0934 AC XY: 6950 AN XY: 74434

Gnomad4 AFR AF: 0.0275

Gnomad4 AMR AF: 0.0781

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.0721

Alfa AF: 0.122 Hom.: 166

Bravo AF: 0.0883

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41490645; hg19: chr3-46410137;