chr3-46368545-G-A

Position:

• chr3-46368545-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125406.1(CCR5AS):​n.565+2699C>T variant causes a intron, non coding transcript 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 NR_125406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CCR5AS	NR_125406.1	n.565+2699C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR5AS	ENST00000701879.1	n.347+2699C>T		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.565+2699C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.755

Alfa AF: 0.738 Hom.: 9277

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7637813; hg19: chr3-46410036;