rs6441975

chr3-46386699-A-Cchr3-46386699-A-Gchr3-46386699-A-T

Variant summary

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

The NR_125406.1(CCR5AS):n.391+6126T>G 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 0.757 in 152,100 control chromosomes in the GnomAD database, including 44,414 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 0.76 (44414 hom., cov: 32)
• Consequence: CCR5AS NR_125406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR5AS	NR_125406.1	n.391+6126T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR5AS	ENST00000701879.1	n.174-15282T>G		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.391+6126T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115073 AN: 151982 Hom.: 44351 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.757 AC: 115181 AN: 152100 Hom.: 44414 Cov.: 32 AF XY: 0.758 AC XY: 56409 AN XY: 74382

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.737

Alfa AF: 0.692 Hom.: 40092

Bravo AF: 0.770

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.7
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6441975; hg19: chr3-46428190;