rs2734225

Variant names:

• chr3-46369445-G-T
• rs2734225
• ENST00000451485.3:n.572+1799C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000451485.3(CCR5AS):​n.572+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 ENST00000451485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451485.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR5AS	NR_125406.2	MANE Select	n.572+1799C>A		intron	N/A
	CCR5AS	NR_185891.1		n.344+1799C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCR5AS	ENST00000451485.3	TSL:3 MANE Select	n.572+1799C>A		intron	N/A
	CCR5AS	ENST00000701879.2		n.462+1799C>A		intron	N/A
	CCR5AS	ENST00000717843.1		n.324+1799C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45223 AN: 149032 Hom.: 7822 Cov.: 26

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.: 26 AF XY: 0.308 AC XY: 22375 AN XY: 72718

African (AFR) AF: 0.128 AC: 5179 AN: 40310

American (AMR) AF: 0.379 AC: 5666 AN: 14960

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1294 AN: 3446

East Asian (EAS) AF: 0.562 AC: 2850 AN: 5068

South Asian (SAS) AF: 0.417 AC: 1966 AN: 4710

European-Finnish (FIN) AF: 0.317 AC: 3185 AN: 10052

Middle Eastern (MID) AF: 0.428 AC: 124 AN: 290

European-Non Finnish (NFE) AF: 0.356 AC: 23946 AN: 67350

Other (OTH) AF: 0.348 AC: 718 AN: 2062

Alfa AF: 0.235 Hom.: 1101

Bravo AF: 0.296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.47
PhyloP100		0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2734225;

hg19: chr3-46410936;