chr3-46367622-G-A

Variant names:

• chr3-46367622-G-A
• rs3136535
• ENST00000451485.3:n.573-2577C>T

Variant summary

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

The ENST00000451485.3(CCR5AS):​n.573-2577C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,230 control chromosomes in the GnomAD database, including 1,041 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 0.11 (1041 hom., cov: 32)
• Consequence: CCR5AS ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR5AS	NR_125406.2	MANE Select	n.573-2577C>T		intron	N/A
	CCR5AS	NR_185891.1		n.345-2577C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR5AS	ENST00000451485.3	TSL:3 MANE Select	n.573-2577C>T		intron	N/A
	CCR5AS	ENST00000701879.2		n.463-2577C>T		intron	N/A
	CCR5AS	ENST00000717843.1		n.325-338C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16120 AN: 152112 Hom.: 1041 Cov.: 32

Gnomad AFR AF: 0.0599

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.0816

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.106 AC: 16128 AN: 152230 Hom.: 1041 Cov.: 32 AF XY: 0.103 AC XY: 7675 AN XY: 74430

African (AFR) AF: 0.0597 AC: 2481 AN: 41534

American (AMR) AF: 0.0817 AC: 1249 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0236 AC: 114 AN: 4826

European-Finnish (FIN) AF: 0.151 AC: 1600 AN: 10596

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9664 AN: 68008

Other (OTH) AF: 0.0838 AC: 177 AN: 2112

Alfa AF: 0.124 Hom.: 168

Bravo AF: 0.0999

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs3136535; hg19: chr3-46409113;