Variant rs3743500 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000351217.10(NPTN):c.-226T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 397,134 control chromosomes in the GnomAD database, including 51,528 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 0.49 ( 18531 hom., cov: 32)

Exomes 𝑓: 0.52 ( 32997 hom. )

Consequence

NPTN
ENST00000351217.10 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.501

Variant links:

Genes affected

NPTN (HGNC:17867): (neuroplastin) This gene encodes a type I transmembrane protein belonging to the Ig superfamily. The protein is believed to be involved in cell-cell interactions or cell-substrate interactions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2009]

NPTN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPTN	ENST00000351217.10 linkuse as main transcript	c.-226T>G		5_prime_UTR_variant	1/8	1		ENSP00000342958		Q9Y639-1

Frequencies

GnomAD3 genomes

AF:

0.490

AC:

74446

AN:

151802

Hom.:

18518

Cov.:

show subpopulations

Gnomad AFR

AF:

0.422

Gnomad AMI

AF:

0.597

Gnomad AMR

AF:

0.527

Gnomad ASJ

AF:

0.455

Gnomad EAS

AF:

0.531

Gnomad SAS

AF:

0.447

Gnomad FIN

AF:

0.528

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.480

GnomAD4 exome

AF:

0.516

AC:

126459

AN:

245214

Hom.:

32997

Cov.:

AF XY:

0.514

AC XY:

65006

AN XY:

126554

show subpopulations

Gnomad4 AFR exome

AF:

0.424

Gnomad4 AMR exome

AF:

0.529

Gnomad4 ASJ exome

AF:

0.452

Gnomad4 EAS exome

AF:

0.595

Gnomad4 SAS exome

AF:

0.432

Gnomad4 FIN exome

AF:

0.535

Gnomad4 NFE exome

AF:

0.516

Gnomad4 OTH exome

AF:

0.501

GnomAD4 genome

AF:

0.490

AC:

74515

AN:

151920

Hom.:

18531

Cov.:

AF XY:

0.492

AC XY:

36534

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.422

Gnomad4 AMR

AF:

0.528

Gnomad4 ASJ

AF:

0.455

Gnomad4 EAS

AF:

0.532

Gnomad4 SAS

AF:

0.446

Gnomad4 FIN

AF:

0.528

Gnomad4 NFE

AF:

0.519

Gnomad4 OTH

AF:

0.480

Alfa

AF:

0.353

Hom.:

912

Bravo

AF:

0.489

Asia WGS

AF:

0.465

AC:

1621

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.86

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