rs2734225

chr3-46369445-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_125406.1(CCR5AS):n.565+1799C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 (7824 hom., cov: 26)
  • Failed GnomAD Quality Control
• Consequence: CCR5AS NR_125406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR5AS	NR_125406.1	n.565+1799C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR5AS	ENST00000701879.1	n.347+1799C>A		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.565+1799C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 45223 AN: 149032 Hom.: 7822 Cov.: 26 FAILED QC

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.351

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.303 AC: 45230 AN: 149148 Hom.: 7824 Cov.: 26 AF XY: 0.308 AC XY: 22375 AN XY: 72718

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.348

Alfa AF: 0.302 Hom.: 940

Bravo AF: 0.296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.8
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2734225; hg19: chr3-46410936;