Genetic Variant NCR2:c.53-20G>A (chr6-41336067-G-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_004828.4(NCR2):c.53-20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0847 in 1,608,032 control chromosomes in the GnomAD database, including 7,998 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 0.11 ( 1269 hom., cov: 32)

Exomes 𝑓: 0.082 ( 6729 hom. )

Consequence

NCR2
NM_004828.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.994

Publications

12 publications found

Variant links:

Genes affected

NCR2 (HGNC:6732): (natural cytotoxicity triggering receptor 2) Predicted to enable signaling receptor activity. Predicted to be involved in cellular defense response and signal transduction. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. Predicted to be active in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

NCR2 links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004828.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NCR2	NM_004828.4	MANE Select	c.53-20G>A	intron	N/A	NP_004819.2	O95944-1
NCR2	NM_001199509.2		c.53-20G>A	intron	N/A	NP_001186438.1	O95944-2
NCR2	NM_001199510.2		c.53-20G>A	intron	N/A	NP_001186439.1	O95944-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NCR2	ENST00000373089.10	TSL:1 MANE Select	c.53-20G>A	intron	N/A	ENSP00000362181.5	O95944-1
NCR2	ENST00000373086.3	TSL:1	c.53-20G>A	intron	N/A	ENSP00000362178.3	O95944-2
NCR2	ENST00000373083.8	TSL:1	c.53-20G>A	intron	N/A	ENSP00000362175.4	O95944-3

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16913

AN:

152024

Hom.:

1266

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.0450

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.0917

Gnomad FIN

AF:

0.0237

Gnomad MID

AF:

0.185

Gnomad NFE

AF:

0.0712

Gnomad OTH

AF:

0.122

GnomAD2 exomes

AF:

0.101

AC:

25008

AN:

246746

AF XY:

0.0978

show subpopulations

Gnomad AFR exome

AF:

0.177

Gnomad AMR exome

AF:

0.0987

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.323

Gnomad FIN exome

AF:

0.0230

Gnomad NFE exome

AF:

0.0702

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.0819

AC:

119204

AN:

1455888

Hom.:

6729

Cov.:

AF XY:

0.0817

AC XY:

59126

AN XY:

723566

show subpopulations

African (AFR)

AF:

0.180

AC:

5998

AN:

33390

American (AMR)

AF:

0.0995

AC:

4420

AN:

44420

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

3109

AN:

25582

East Asian (EAS)

AF:

0.330

AC:

13093

AN:

39618

South Asian (SAS)

AF:

0.0892

AC:

7622

AN:

85414

European-Finnish (FIN)

AF:

0.0252

AC:

1330

AN:

52854

Middle Eastern (MID)

AF:

0.164

AC:

939

AN:

5730

European-Non Finnish (NFE)

AF:

0.0691

AC:

76601

AN:

1108752

Other (OTH)

AF:

0.101

AC:

6092

AN:

60128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

6461

12921

19382

25842

32303

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3148

6296

9444

12592

15740

<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:

0.111

AC:

16930

AN:

152144

Hom.:

1269

Cov.:

AF XY:

0.111

AC XY:

8255

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.178

AC:

7390

AN:

41474

American (AMR)

AF:

0.107

AC:

1641

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.120

AC:

417

AN:

3466

East Asian (EAS)

AF:

0.306

AC:

1573

AN:

5138

South Asian (SAS)

AF:

0.0913

AC:

441

AN:

4828

European-Finnish (FIN)

AF:

0.0237

AC:

252

AN:

10612

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0712

AC:

4844

AN:

68014

Other (OTH)

AF:

0.130

AC:

274

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

755

1511

2266

3022

3777

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<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:

0.0953

Hom.:

1002

Bravo

AF:

0.122

Asia WGS

AF:

0.209

AC:

727

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.2

(source)

DANN

Benign

0.40

PhyloP100

-0.99

PromoterAI

-0.012

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over