rs11575815

chr3-46378679-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.392-7262T>A 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 0.301 in 152,076 control chromosomes in the GnomAD database, including 7,858 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 (7858 hom., cov: 32)
• Consequence: CCR5AS NR_125406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR5AS	NR_125406.1	n.392-7262T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR5AS	ENST00000701879.1	n.174-7262T>A		intron_variant, non_coding_transcript_variant
CCR5AS	ENST00000451485.2	n.392-7262T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45790 AN: 151960 Hom.: 7859 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.418

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: 45792 AN: 152076 Hom.: 7858 Cov.: 32 AF XY: 0.305 AC XY: 22662 AN XY: 74340

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.347

Alfa AF: 0.302 Hom.: 941

Bravo AF: 0.298

Asia WGS AF: 0.419 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.5
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11575815; hg19: chr3-46420170;