Variant 14-24408493-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.823A>G(p.Ser275Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 1,598,136 control chromosomes in the GnomAD database, including 1,208 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.044 ( 380 hom., cov: 33)

Exomes 𝑓: 0.012 ( 828 hom. )

Consequence

NYNRIN
NM_025081.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.505

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 (MetaRNN=0.001491636).

BP6

Variant 14-24408493-A-G is Benign according to our data. Variant chr14-24408493-A-G is described in ClinVar as [Benign]. Clinvar id is 2847366.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 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.823A>G	p.Ser275Gly	missense_variant	3/9	ENST00000382554.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NYNRIN	ENST00000382554.4 linkuse as main transcript	c.823A>G	p.Ser275Gly	missense_variant	3/9	5	NM_025081.3	P1	Q9P2P1-1

Frequencies

GnomAD3 genomes

AF:

0.0440

AC:

6686

AN:

152118

Hom.:

379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0291

Gnomad ASJ

AF:

0.00375

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.0743

Gnomad FIN

AF:

0.00226

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00121

Gnomad OTH

AF:

0.0282

GnomAD3 exomes

AF:

0.0302

AC:

7050

AN:

233690

Hom.:

352

AF XY:

0.0285

AC XY:

3625

AN XY:

127294

show subpopulations

Gnomad AFR exome

AF:

0.122

Gnomad AMR exome

AF:

0.0278

Gnomad ASJ exome

AF:

0.00271

Gnomad EAS exome

AF:

0.124

Gnomad SAS exome

AF:

0.0662

Gnomad FIN exome

AF:

0.00337

Gnomad NFE exome

AF:

0.000975

Gnomad OTH exome

AF:

0.0198

GnomAD4 exome

AF:

0.0121

AC:

17496

AN:

1445900

Hom.:

828

Cov.:

AF XY:

0.0131

AC XY:

9387

AN XY:

717714

show subpopulations

Gnomad4 AFR exome

AF:

0.121

Gnomad4 AMR exome

AF:

0.0298

Gnomad4 ASJ exome

AF:

0.00289

Gnomad4 EAS exome

AF:

0.113

Gnomad4 SAS exome

AF:

0.0632

Gnomad4 FIN exome

AF:

0.00354

Gnomad4 NFE exome

AF:

0.000702

Gnomad4 OTH exome

AF:

0.0226

GnomAD4 genome

AF:

0.0440

AC:

6693

AN:

152236

Hom.:

380

Cov.:

AF XY:

0.0444

AC XY:

3306

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.0292

Gnomad4 ASJ

AF:

0.00375

Gnomad4 EAS

AF:

0.129

Gnomad4 SAS

AF:

0.0733

Gnomad4 FIN

AF:

0.00226

Gnomad4 NFE

AF:

0.00121

Gnomad4 OTH

AF:

0.0274

Alfa

AF:

0.0119

Hom.:

156

Bravo

AF:

0.0480

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.00156

AC:

ESP6500AA

AF:

0.0954

AC:

401

ESP6500EA

AF:

0.00154

AC:

ExAC

AF:

0.0305

AC:

3683

Asia WGS

AF:

0.100

AC:

347

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

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.063

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.94

DEOGEN2

Benign

0.011

Eigen

Benign

-0.90

Eigen_PC

Benign

-0.86

FATHMM_MKL

Benign

0.038

LIST_S2

Benign

0.43

MetaRNN

Benign

0.0015

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.5

MutationTaster

Benign

1.0

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.010

REVEL

Benign

0.15

Sift

Uncertain

0.0010

Sift4G

Uncertain

0.029

Polyphen

0.0

Vest4

0.039

MPC

0.18

ClinPred

0.023

GERP RS

3.8

Varity_R

0.12

gMVP

0.13

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

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