NM_004829.7:c.244C>A

Variant summary

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

The NM_004829.7(NCR1):​c.244C>A​(p.Gln82Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.902 in 1,614,136 control chromosomes in the GnomAD database, including 659,633 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.91 ( 63021 hom., cov: 32)
Exomes 𝑓: 0.90 ( 596612 hom. )

Consequence

NCR1
NM_004829.7 missense

Scores

5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.756

Publications

31 publications found
Variant links:
Genes affected
NCR1 (HGNC:6731): (natural cytotoxicity triggering receptor 1) Predicted to be involved in cellular defense response; regulation of natural killer cell mediated cytotoxicity; and signal transduction. Predicted to act upstream of or within defense response to virus and detection of virus. Predicted to be located in cell surface. Predicted to be part of SWI/SNF complex. Predicted to be active in plasma membrane. Biomarker of acquired immunodeficiency syndrome; anogenital venereal wart; hepatitis C; and lymphoproliferative syndrome. [provided by Alliance of Genome Resources, Apr 2022]

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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 (MetaRNN=0.005638659).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NCR1NM_004829.7 linkc.244C>A p.Gln82Lys missense_variant Exon 3 of 7 ENST00000291890.9 NP_004820.2 O76036A0A0A0MQZ0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NCR1ENST00000291890.9 linkc.244C>A p.Gln82Lys missense_variant Exon 3 of 7 5 NM_004829.7 ENSP00000291890.3 A0A0A0MQZ0

Frequencies

GnomAD3 genomes
AF:
0.907
AC:
137965
AN:
152134
Hom.:
62966
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.965
Gnomad AMI
AF:
0.956
Gnomad AMR
AF:
0.837
Gnomad ASJ
AF:
0.867
Gnomad EAS
AF:
0.630
Gnomad SAS
AF:
0.776
Gnomad FIN
AF:
0.893
Gnomad MID
AF:
0.807
Gnomad NFE
AF:
0.922
Gnomad OTH
AF:
0.889
GnomAD4 exome
AF:
0.901
AC:
1317161
AN:
1461884
Hom.:
596612
Cov.:
90
AF XY:
0.898
AC XY:
653158
AN XY:
727244
show subpopulations
African (AFR)
AF:
0.967
AC:
32390
AN:
33480
American (AMR)
AF:
0.770
AC:
34448
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
0.864
AC:
22588
AN:
26136
East Asian (EAS)
AF:
0.616
AC:
24442
AN:
39700
South Asian (SAS)
AF:
0.805
AC:
69471
AN:
86258
European-Finnish (FIN)
AF:
0.900
AC:
48054
AN:
53410
Middle Eastern (MID)
AF:
0.803
AC:
4634
AN:
5768
European-Non Finnish (NFE)
AF:
0.924
AC:
1027753
AN:
1112012
Other (OTH)
AF:
0.884
AC:
53381
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.520
Heterozygous variant carriers
0
9542
19084
28627
38169
47711
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
21468
42936
64404
85872
107340
<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:
0.907
AC:
138077
AN:
152252
Hom.:
63021
Cov.:
32
AF XY:
0.901
AC XY:
67068
AN XY:
74430
show subpopulations
African (AFR)
AF:
0.965
AC:
40114
AN:
41556
American (AMR)
AF:
0.837
AC:
12799
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
0.867
AC:
3009
AN:
3472
East Asian (EAS)
AF:
0.630
AC:
3249
AN:
5160
South Asian (SAS)
AF:
0.777
AC:
3744
AN:
4818
European-Finnish (FIN)
AF:
0.893
AC:
9465
AN:
10604
Middle Eastern (MID)
AF:
0.799
AC:
235
AN:
294
European-Non Finnish (NFE)
AF:
0.922
AC:
62714
AN:
68022
Other (OTH)
AF:
0.887
AC:
1876
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
632
1263
1895
2526
3158
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
902
1804
2706
3608
4510
<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:
0.910
Hom.:
216502
Bravo
AF:
0.907

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.060
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.0080
DEOGEN2
Benign
0.00049
.;T;T;T
MetaRNN
Benign
0.0056
T;T;T;T
PhyloP100
-0.76
Sift4G
Benign
1.0
T;T;T;T
Vest4
0.12
gMVP
0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2278428; hg19: chr19-55418054; API