chr3-46368545-G-A

Variant names:

• chr3-46368545-G-A
• rs7637813
• ENST00000451485.3:n.572+2699C>T

Variant summary

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

The ENST00000451485.3(CCR5AS):​n.572+2699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,184 control chromosomes in the GnomAD database, including 46,021 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 0.77 (46021 hom., cov: 32)
• Consequence: CCR5AS ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR5AS	NR_125406.2	n.572+2699C>T		intron_variant	Intron 3 of 3
CCR5AS	NR_185891.1	n.344+2699C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR5AS	ENST00000451485.3	n.572+2699C>T		intron_variant	Intron 3 of 3	3
CCR5AS	ENST00000701879.2	n.462+2699C>T		intron_variant	Intron 2 of 2
CCR5AS	ENST00000717843.1	n.325-1261C>T		intron_variant	Intron 2 of 3
CCR5AS	ENST00000741276.1	n.335+2699C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117321 AN: 152066 Hom.: 45959 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.772 AC: 117426 AN: 152184 Hom.: 46021 Cov.: 32 AF XY: 0.772 AC XY: 57423 AN XY: 74392

African (AFR) AF: 0.909 AC: 37773 AN: 41558

American (AMR) AF: 0.756 AC: 11558 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2675 AN: 3466

East Asian (EAS) AF: 0.803 AC: 4160 AN: 5178

South Asian (SAS) AF: 0.764 AC: 3689 AN: 4826

European-Finnish (FIN) AF: 0.681 AC: 7189 AN: 10564

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47804 AN: 67992

Other (OTH) AF: 0.755 AC: 1593 AN: 2110

Alfa AF: 0.744 Hom.: 16422

Bravo AF: 0.784

Asia WGS AF: 0.758 AC: 2636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.21
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Publications

Loading publications...

Other links and lift over

dbSNP: rs7637813; hg19: chr3-46410036;