3-46369003-A-C

Variant names:

• chr3-46369003-A-C
• rs2856757
• ENST00000451485.3:n.572+2241T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000451485.3(CCR5AS):​n.572+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 ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451485.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR5AS	NR_125406.2	MANE Select	n.572+2241T>G		intron	N/A
	CCR5AS	NR_185891.1		n.344+2241T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR5AS	ENST00000451485.3	TSL:3 MANE Select	n.572+2241T>G		intron	N/A
	CCR5AS	ENST00000701879.2		n.462+2241T>G		intron	N/A
	CCR5AS	ENST00000717843.1		n.325-1719T>G		intron	N/A

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

African (AFR) AF: 0.133 AC: 5502 AN: 41520

American (AMR) AF: 0.397 AC: 6068 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2858 AN: 5178

South Asian (SAS) AF: 0.420 AC: 2027 AN: 4822

European-Finnish (FIN) AF: 0.313 AC: 3305 AN: 10576

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26249 AN: 67946

Other (OTH) AF: 0.366 AC: 772 AN: 2108

Alfa AF: 0.350 Hom.: 12838

Bravo AF: 0.316

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.48
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2856757; hg19: chr3-46410494; COSMIC: COSV52753176;