Genetic Variant FLT1P1:n.445G>C (chr3-46143233-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000451650.1(FLT1P1):n.445G>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.114 in 789,390 control chromosomes in the GnomAD database, including 6,931 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 0.097 ( 831 hom., cov: 32)

Exomes 𝑓: 0.12 ( 6100 hom. )

Consequence

FLT1P1
ENST00000451650.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.13

Publications

11 publications found

Variant links:

Genes affected

FLT1P1 (HGNC:44609): (FLT1 pseudogene 1)

FLT1P1 links:

CCR3 (HGNC:1604): (C-C motif chemokine receptor 3) The protein encoded by this gene is a receptor for C-C type chemokines. It belongs to family 1 of the G protein-coupled receptors. This receptor binds and responds to a variety of chemokines, including eotaxin (CCL11), eotaxin-3 (CCL26), MCP-3 (CCL7), MCP-4 (CCL13), and RANTES (CCL5). It is highly expressed in eosinophils and basophils, and is also detected in TH1 and TH2 cells, as well as in airway epithelial cells. This receptor may contribute to the accumulation and activation of eosinophils and other inflammatory cells in the allergic airway. It is also known to be an entry co-receptor for HIV-1. This gene and seven other chemokine receptor genes form a chemokine receptor gene cluster on the chromosomal region 3p21. Alternatively spliced transcript variants have been described. [provided by RefSeq, Sep 2009]

CCR3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLT1P1		n.46143233C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLT1P1	ENST00000451650.1 link	n.445G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
CCR3	ENST00000684109.1 link	n.691+11653C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0969

AC:

14750

AN:

152150

Hom.:

829

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.0628

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.0448

Gnomad SAS

AF:

0.275

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.0816

Gnomad OTH

AF:

0.0855

GnomAD4 exome

AF:

0.118

AC:

74983

AN:

637122

Hom.:

6100

Cov.:

AF XY:

0.127

AC XY:

43844

AN XY:

346038

show subpopulations

African (AFR)

AF:

0.111

AC:

1976

AN:

17846

American (AMR)

AF:

0.0556

AC:

2379

AN:

42768

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

2344

AN:

20752

East Asian (EAS)

AF:

0.0477

AC:

1711

AN:

35858

South Asian (SAS)

AF:

0.280

AC:

19727

AN:

70340

European-Finnish (FIN)

AF:

0.154

AC:

7913

AN:

51400

Middle Eastern (MID)

AF:

0.158

AC:

635

AN:

4026

European-Non Finnish (NFE)

AF:

0.0964

AC:

34800

AN:

361070

Other (OTH)

AF:

0.106

AC:

3498

AN:

33062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.563

Heterozygous variant carriers

3460

6920

10380

13840

17300

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

508

1016

1524

2032

2540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0969

AC:

14762

AN:

152268

Hom.:

831

Cov.:

AF XY:

0.104

AC XY:

7715

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.102

AC:

4243

AN:

41552

American (AMR)

AF:

0.0627

AC:

959

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

383

AN:

3472

East Asian (EAS)

AF:

0.0447

AC:

232

AN:

5186

South Asian (SAS)

AF:

0.275

AC:

1329

AN:

4824

European-Finnish (FIN)

AF:

0.158

AC:

1679

AN:

10598

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0816

AC:

5548

AN:

68010

Other (OTH)

AF:

0.0851

AC:

180

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

659

1318

1977

2636

3295

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0437

Hom.:

Bravo

AF:

0.0860

Asia WGS

AF:

0.147

AC:

510

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.44

PhyloP100

4.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over