Variant chr14-24407858-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_025081.3(NYNRIN):c.199-11A>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0346 in 1,588,916 control chromosomes in the GnomAD database, including 1,966 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.031 ( 188 hom., cov: 33)

Exomes 𝑓: 0.035 ( 1778 hom. )

Consequence

NYNRIN
NM_025081.3 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00001716

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.171

Variant links:

Genes affected

NYNRIN (HGNC:20165): (NYN domain and retroviral integrase containing) Predicted to enable endoribonuclease activity and mRNA binding activity. Predicted to be involved in RNA phosphodiester bond hydrolysis, endonucleolytic. Predicted to be integral component of membrane. Predicted to be active in cytoplasmic ribonucleoprotein granule and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

NYNRIN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 14-24407858-A-G is Benign according to our data. Variant chr14-24407858-A-G is described in ClinVar as [Benign]. Clinvar id is 2798126.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NYNRIN	NM_025081.3 linkuse as main transcript	c.199-11A>G		splice_polypyrimidine_tract_variant, intron_variant		ENST00000382554.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NYNRIN	ENST00000382554.4 linkuse as main transcript	c.199-11A>G		splice_polypyrimidine_tract_variant, intron_variant		5	NM_025081.3	P1	Q9P2P1-1

Frequencies

GnomAD3 genomes

AF:

0.0312

AC:

4751

AN:

152158

Hom.:

187

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00700

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0228

Gnomad ASJ

AF:

0.0233

Gnomad EAS

AF:

0.234

Gnomad SAS

AF:

0.0367

Gnomad FIN

AF:

0.0603

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0285

Gnomad OTH

AF:

0.0292

GnomAD3 exomes

AF:

0.0442

AC:

10216

AN:

231312

Hom.:

605

AF XY:

0.0441

AC XY:

5534

AN XY:

125348

show subpopulations

Gnomad AFR exome

AF:

0.00628

Gnomad AMR exome

AF:

0.0109

Gnomad ASJ exome

AF:

0.0214

Gnomad EAS exome

AF:

0.240

Gnomad SAS exome

AF:

0.0358

Gnomad FIN exome

AF:

0.0610

Gnomad NFE exome

AF:

0.0283

Gnomad OTH exome

AF:

0.0332

GnomAD4 exome

AF:

0.0350

AC:

50259

AN:

1436640

Hom.:

1778

Cov.:

AF XY:

0.0349

AC XY:

24833

AN XY:

712238

show subpopulations

Gnomad4 AFR exome

AF:

0.00548

Gnomad4 AMR exome

AF:

0.0115

Gnomad4 ASJ exome

AF:

0.0237

Gnomad4 EAS exome

AF:

0.226

Gnomad4 SAS exome

AF:

0.0359

Gnomad4 FIN exome

AF:

0.0561

Gnomad4 NFE exome

AF:

0.0287

Gnomad4 OTH exome

AF:

0.0432

GnomAD4 genome

AF:

0.0312

AC:

4753

AN:

152276

Hom.:

188

Cov.:

AF XY:

0.0332

AC XY:

2473

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.00698

Gnomad4 AMR

AF:

0.0228

Gnomad4 ASJ

AF:

0.0233

Gnomad4 EAS

AF:

0.234

Gnomad4 SAS

AF:

0.0365

Gnomad4 FIN

AF:

0.0603

Gnomad4 NFE

AF:

0.0285

Gnomad4 OTH

AF:

0.0317

Alfa

AF:

0.0250

Hom.:

Bravo

AF:

0.0282

Asia WGS

AF:

0.111

AC:

383

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.067

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000017

dbscSNV1_RF

Benign

0.0

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over