dbSNP rs11575839: NCR3:p.Ser52Ser (chr6-31590014-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_147130.3(NCR3):c.156C>T(p.Ser52Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0341 in 1,612,980 control chromosomes in the GnomAD database, including 2,111 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 0.048 ( 275 hom., cov: 32)

Exomes 𝑓: 0.033 ( 1836 hom. )

Consequence

NCR3
NM_147130.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.98

Publications

33 publications found

Variant links:

Genes affected

NCR3 (HGNC:19077): (natural cytotoxicity triggering receptor 3) The protein encoded by this gene is a natural cytotoxicity receptor (NCR) that may aid NK cells in the lysis of tumor cells. The encoded protein interacts with CD3-zeta (CD247), a T-cell receptor. A single nucleotide polymorphism in the 5' untranslated region of this gene has been associated with mild malaria suceptibility. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]

NCR3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP7

Synonymous conserved (PhyloP=-1.98 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCR3	NM_147130.3 link	c.156C>T	p.Ser52Ser	synonymous_variant	Exon 2 of 4	ENST00000340027.10	NP_667341.1	O14931-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCR3	ENST00000340027.10 link	c.156C>T	p.Ser52Ser	synonymous_variant	Exon 2 of 4	1	NM_147130.3	ENSP00000342156.5		O14931-1

Frequencies

GnomAD3 genomes

AF:

0.0478

AC:

7267

AN:

152090

Hom.:

274

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0787

Gnomad AMI

AF:

0.00879

Gnomad AMR

AF:

0.0464

Gnomad ASJ

AF:

0.0262

Gnomad EAS

AF:

0.0385

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.0252

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0269

Gnomad OTH

AF:

0.0531

GnomAD2 exomes

AF:

0.0481

AC:

11823

AN:

245566

AF XY:

0.0540

show subpopulations

Gnomad AFR exome

AF:

0.0781

Gnomad AMR exome

AF:

0.0254

Gnomad ASJ exome

AF:

0.0296

Gnomad EAS exome

AF:

0.0515

Gnomad FIN exome

AF:

0.0271

Gnomad NFE exome

AF:

0.0274

Gnomad OTH exome

AF:

0.0432

GnomAD4 exome

AF:

0.0327

AC:

47704

AN:

1460772

Hom.:

1836

Cov.:

AF XY:

0.0367

AC XY:

26699

AN XY:

726700

show subpopulations

African (AFR)

AF:

0.0791

AC:

2649

AN:

33480

American (AMR)

AF:

0.0275

AC:

1230

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0262

AC:

684

AN:

26136

East Asian (EAS)

AF:

0.0346

AC:

1374

AN:

39700

South Asian (SAS)

AF:

0.155

AC:

13368

AN:

86258

European-Finnish (FIN)

AF:

0.0276

AC:

1442

AN:

52316

Middle Eastern (MID)

AF:

0.0548

AC:

316

AN:

5766

European-Non Finnish (NFE)

AF:

0.0217

AC:

24123

AN:

1112008

Other (OTH)

AF:

0.0417

AC:

2518

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

3084

6167

9251

12334

15418

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

964

1928

2892

3856

4820

<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:

0.0479

AC:

7291

AN:

152208

Hom.:

275

Cov.:

AF XY:

0.0502

AC XY:

3733

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0791

AC:

3286

AN:

41530

American (AMR)

AF:

0.0463

AC:

707

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0262

AC:

AN:

3472

East Asian (EAS)

AF:

0.0384

AC:

199

AN:

5184

South Asian (SAS)

AF:

0.160

AC:

771

AN:

4818

European-Finnish (FIN)

AF:

0.0252

AC:

267

AN:

10616

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0269

AC:

1831

AN:

68002

Other (OTH)

AF:

0.0539

AC:

114

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

336

673

1009

1346

1682

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0342

Hom.:

370

Bravo

AF:

0.0475

Asia WGS

AF:

0.115

AC:

397

AN:

3478

EpiCase

AF:

0.0264

EpiControl

AF:

0.0306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.55

(source)

DANN

Benign

0.79

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over