dbSNP rs2273635: NYNRIN:c.2642+64T>A (chr14-24411514-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_025081.3(NYNRIN):c.2642+64T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 1,392,164 control chromosomes in the GnomAD database, including 635 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 0.013 ( 73 hom., cov: 32)

Exomes 𝑓: 0.010 ( 562 hom. )

Consequence

NYNRIN
NM_025081.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.02

Publications

4 publications found

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 was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

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 rank	MANE	Protein	UniProt
NYNRIN	NM_025081.3 link	c.2642+64T>A		intron_variant	Intron 6 of 8	ENST00000382554.4	NP_079357.2
NYNRIN	XM_011537016.2 link	c.-1176T>A		5_prime_UTR_variant	Exon 1 of 4		XP_011535318.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NYNRIN	ENST00000382554.4 link	c.2642+64T>A		intron_variant	Intron 6 of 8	5	NM_025081.3	ENSP00000371994.3

Frequencies

GnomAD3 genomes

AF:

0.0131

AC:

1986

AN:

151974

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0144

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0166

Gnomad ASJ

AF:

0.00374

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.0743

Gnomad FIN

AF:

0.00226

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.000898

Gnomad OTH

AF:

0.00768

GnomAD4 exome

AF:

0.0100

AC:

12450

AN:

1240074

Hom.:

562

AF XY:

0.0115

AC XY:

7223

AN XY:

627494

show subpopulations

African (AFR)

AF:

0.0133

AC:

384

AN:

28846

American (AMR)

AF:

0.0230

AC:

1006

AN:

43680

Ashkenazi Jewish (ASJ)

AF:

0.00265

AC:

AN:

24498

East Asian (EAS)

AF:

0.112

AC:

4347

AN:

38738

South Asian (SAS)

AF:

0.0622

AC:

5099

AN:

81928

European-Finnish (FIN)

AF:

0.00349

AC:

179

AN:

51262

Middle Eastern (MID)

AF:

0.00374

AC:

AN:

5350

European-Non Finnish (NFE)

AF:

0.000560

AC:

511

AN:

912682

Other (OTH)

AF:

0.0158

AC:

839

AN:

53090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

652

1304

1955

2607

3259

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

162

324

486

648

810

<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:

0.0130

AC:

1978

AN:

152090

Hom.:

Cov.:

AF XY:

0.0150

AC XY:

1112

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.0144

AC:

597

AN:

41500

American (AMR)

AF:

0.0167

AC:

256

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00374

AC:

AN:

3472

East Asian (EAS)

AF:

0.128

AC:

659

AN:

5156

South Asian (SAS)

AF:

0.0733

AC:

352

AN:

4804

European-Finnish (FIN)

AF:

0.00226

AC:

AN:

10606

Middle Eastern (MID)

AF:

0.00342

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000898

AC:

AN:

67956

Other (OTH)

AF:

0.00713

AC:

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

185

278

370

463

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

150

<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:

0.00540

Hom.:

Bravo

AF:

0.0129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

1.2

(source)

DANN

Benign

0.88

PhyloP100

-3.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over