chr3-46378613-C-T

Variant names:

• chr3-46378613-C-T
• rs11575816
• ENST00000451485.3:n.399-7196G>A

Variant summary

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

The ENST00000451485.3(CCR5AS):​n.399-7196G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,142 control chromosomes in the GnomAD database, including 7,863 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 0.30 (7863 hom., cov: 32)
• Consequence: CCR5AS ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.541 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.399-7196G>A		intron	N/A
	CCR5AS	NR_185891.1		n.171-7196G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR5AS	ENST00000451485.3	TSL:3 MANE Select	n.399-7196G>A		intron	N/A
	CCR5AS	ENST00000701879.2		n.289-7196G>A		intron	N/A
	CCR5AS	ENST00000717843.1		n.151-7196G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45817 AN: 152024 Hom.: 7864 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.301 AC: 45820 AN: 152142 Hom.: 7863 Cov.: 32 AF XY: 0.305 AC XY: 22667 AN XY: 74342

African (AFR) AF: 0.126 AC: 5250 AN: 41514

American (AMR) AF: 0.378 AC: 5772 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3470

East Asian (EAS) AF: 0.558 AC: 2891 AN: 5178

South Asian (SAS) AF: 0.416 AC: 2005 AN: 4818

European-Finnish (FIN) AF: 0.307 AC: 3248 AN: 10568

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24164 AN: 68006

Other (OTH) AF: 0.347 AC: 733 AN: 2110

Alfa AF: 0.320 Hom.: 3810

Bravo AF: 0.298

Asia WGS AF: 0.419 AC: 1458 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	1.6
DANN	Benign	0.60
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs11575816; hg19: chr3-46420104;