rs1799988

Positions:

• chr3-46370768-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.565+476G>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 0.492 in 151,988 control chromosomes in the GnomAD database, including 18,629 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 0.49 (18629 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CCR5AS NR_125406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769

Genes affected

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

CCR5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR5AS	NR_125406.1	n.565+476G>A		intron_variant, non_coding_transcript_variant
CCR5	NM_000579.4	c.-232C>T		5_prime_UTR_variant	2/3
CCR5	NM_001100168.2	c.-65-167C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR5AS	ENST00000701879.1	n.347+476G>A		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.565+476G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74711 AN: 151870 Hom.: 18608 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.492 AC: 74767 AN: 151988 Hom.: 18629 Cov.: 32 AF XY: 0.497 AC XY: 36897 AN XY: 74282

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.491

Alfa AF: 0.459 Hom.: 2602

Bravo AF: 0.493

Asia WGS AF: 0.535 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.33
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1799988; hg19: chr3-46412259; COSMIC: COSV52753248;