Genetic Variant NPTXR:c.*3840C>A (chr22-38818769-G-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_014293.4(NPTXR):c.*3840C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,184 control chromosomes in the GnomAD database, including 1,980 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 0.16 ( 1979 hom., cov: 32)

Exomes 𝑓: 0.11 ( 1 hom. )

Consequence

NPTXR
NM_014293.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.610

Publications

9 publications found

Variant links:

Genes affected

NPTXR (HGNC:7954): (neuronal pentraxin receptor) This gene encodes a protein similar to the rat neuronal pentraxin receptor. The rat pentraxin receptor is an integral membrane protein that is thought to mediate neuronal uptake of the snake venom toxin, taipoxin, and its transport into the synapses. Studies in rat indicate that translation of this mRNA initiates at a non-AUG (CUG) codon. This may also be true for mouse and human, based on strong sequence conservation amongst these species. [provided by RefSeq, Jul 2008]

NPTXR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPTXR	NM_014293.4 link	c.*3840C>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000333039.4	NP_055108.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPTXR	ENST00000333039.4 link	c.*3840C>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_014293.4	ENSP00000327545.3
NPTXR	ENST00000718437.1 link	c.*3840C>A		3_prime_UTR_variant	Exon 5 of 5			ENSP00000520822.1

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23653

AN:

151906

Hom.:

1980

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.204

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.174

GnomAD4 exome

AF:

0.113

AC:

AN:

160

Hom.:

Cov.:

AF XY:

0.105

AC XY:

AN XY:

114

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.143

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.114

AC:

AN:

132

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.156

AC:

23646

AN:

152024

Hom.:

1979

Cov.:

AF XY:

0.158

AC XY:

11735

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.112

AC:

4648

AN:

41456

American (AMR)

AF:

0.127

AC:

1946

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

709

AN:

3468

East Asian (EAS)

AF:

0.102

AC:

526

AN:

5144

South Asian (SAS)

AF:

0.184

AC:

886

AN:

4816

European-Finnish (FIN)

AF:

0.214

AC:

2259

AN:

10576

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.175

AC:

11922

AN:

67966

Other (OTH)

AF:

0.173

AC:

364

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

975

1949

2924

3898

4873

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.167

Hom.:

2707

Bravo

AF:

0.146

Asia WGS

AF:

0.123

AC:

430

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

0.61

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over