3-46367622-G-A

Position:

• chr3-46367622-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.566-2577C>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 0.106 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 NR_125406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR5AS	NR_125406.1	n.566-2577C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR5AS	ENST00000701879.1	n.348-2577C>T		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.566-2577C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0597

Gnomad4 AMR AF: 0.0817

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.0838

Alfa AF: 0.127 Hom.: 167

Bravo AF: 0.0999

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3136535; hg19: chr3-46409113;