Variant chr3-46369445-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000451485.2(CCR5AS):n.565+1799C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 ( 7824 hom., cov: 26)

Failed GnomAD Quality Control

Consequence

CCR5AS
ENST00000451485.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

Variant links:

Genes affected

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

CCR5AS links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR5AS	NR_125406.2 link	n.572+1799C>A		intron_variant
CCR5AS	NR_185891.1 link	n.344+1799C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCR5AS	ENST00000451485.2 link	n.565+1799C>A		intron_variant		3
CCR5AS	ENST00000701879.1 link	n.347+1799C>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

45223

AN:

149032

Hom.:

7822

Cov.:

FAILED QC

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.336

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.376

Gnomad EAS

AF:

0.563

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.423

Gnomad NFE

AF:

0.355

Gnomad OTH

AF:

0.351

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.303

AC:

45230

AN:

149148

Hom.:

7824

Cov.:

AF XY:

0.308

AC XY:

22375

AN XY:

72718

show subpopulations

Gnomad4 AFR

AF:

0.128

Gnomad4 AMR

AF:

0.379

Gnomad4 ASJ

AF:

0.376

Gnomad4 EAS

AF:

0.562

Gnomad4 SAS

AF:

0.417

Gnomad4 FIN

AF:

0.317

Gnomad4 NFE

AF:

0.356

Gnomad4 OTH

AF:

0.348

Alfa

AF:

0.302

Hom.:

940

Bravo

AF:

0.296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.8

DANN

Benign

0.47

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over