chr3-46367240-G-A

Variant names:

• chr3-46367240-G-A
• rs2040388
• ENST00000717843.1:n.369C>T

Variant summary

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

The ENST00000717843.1(CCR5AS):​n.369C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,796 control chromosomes in the GnomAD database, including 32,442 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 0.64 (32442 hom., cov: 30)
• Consequence: CCR5AS ENST00000717843.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR5AS	NR_125406.2	n.573-2195C>T		intron_variant	Intron 3 of 3
CCR5AS	NR_185891.1	n.345-2195C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR5AS	ENST00000717843.1	n.369C>T		non_coding_transcript_exon_variant	Exon 3 of 4
CCR5AS	ENST00000451485.3	n.573-2195C>T		intron_variant	Intron 3 of 3	3
CCR5AS	ENST00000701879.2	n.463-2195C>T		intron_variant	Intron 2 of 2
CCR5AS	ENST00000741276.1	n.336-2195C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97731 AN: 151680 Hom.: 32400 Cov.: 30

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.644 AC: 97812 AN: 151796 Hom.: 32442 Cov.: 30 AF XY: 0.649 AC XY: 48137 AN XY: 74180

African (AFR) AF: 0.786 AC: 32540 AN: 41406

American (AMR) AF: 0.656 AC: 10019 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1943 AN: 3466

East Asian (EAS) AF: 0.803 AC: 4144 AN: 5160

South Asian (SAS) AF: 0.742 AC: 3551 AN: 4784

European-Finnish (FIN) AF: 0.530 AC: 5554 AN: 10470

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37911 AN: 67926

Other (OTH) AF: 0.649 AC: 1368 AN: 2108

Alfa AF: 0.421 Hom.: 997

Bravo AF: 0.659

Asia WGS AF: 0.725 AC: 2519 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.027
DANN	Benign	0.37
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2040388; hg19: chr3-46408731;