rs2856757

Positions:

• chr3-46369003-A-C
• chr3-46369003-A-T

Variant summary

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

The ENST00000451485.2(CCR5AS):​n.565+2241T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,096 control chromosomes in the GnomAD database, including 8,839 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 0.32 (8839 hom., cov: 32)
• Consequence: CCR5AS ENST00000451485.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

CCR5AS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR5AS	NR_125406.2	n.572+2241T>G		intron_variant
CCR5AS	NR_185891.1	n.344+2241T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR5AS	ENST00000451485.2	n.565+2241T>G		intron_variant		3
CCR5AS	ENST00000701879.1	n.347+2241T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48578 AN: 151978 Hom.: 8838 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.319 AC: 48582 AN: 152096 Hom.: 8839 Cov.: 32 AF XY: 0.322 AC XY: 23934 AN XY: 74350

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.366

Alfa AF: 0.179 Hom.: 394

Bravo AF: 0.316

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
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: rs2856757; hg19: chr3-46410494; COSMIC: COSV52753176;