rs916093

Positions:

• chr3-46403303-T-C

Variant summary

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

The NR_125406.1(CCR5AS):​n.163+3594A>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 0.185 in 152,160 control chromosomes in the GnomAD database, including 3,356 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 0.19 (3356 hom., cov: 32)
• Consequence: CCR5AS NR_125406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR5AS	NR_125406.1	n.163+3594A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR5AS	ENST00000701879.1	n.173+3594A>G		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.163+3594A>G		intron_variant, non_coding_transcript_variant		3
CCR5AS	ENST00000686150.2	n.207+3594A>G		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000691693.2	n.221+3594A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28138 AN: 152042 Hom.: 3345 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.185 AC: 28186 AN: 152160 Hom.: 3356 Cov.: 32 AF XY: 0.179 AC XY: 13310 AN XY: 74396

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0216

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.143

Alfa AF: 0.193 Hom.: 514

Bravo AF: 0.191

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916093; hg19: chr3-46444794;