6-31588932-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_147130.3(NCR3):​c.*135T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 1,028,844 control chromosomes in the GnomAD database, including 5,844 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 0.088 ( 867 hom., cov: 32)
Exomes 𝑓: 0.093 ( 4977 hom. )

Consequence

NCR3
NM_147130.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0690
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]
LST1 (HGNC:14189): (leukocyte specific transcript 1) The protein encoded by this gene is a membrane protein that can inhibit the proliferation of lymphocytes. Expression of this gene is enhanced by lipopolysaccharide, interferon-gamma, and bacteria. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NCR3NM_147130.3 linkuse as main transcriptc.*135T>C 3_prime_UTR_variant 4/4 ENST00000340027.10
LST1NM_205839.3 linkuse as main transcript downstream_gene_variant ENST00000438075.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NCR3ENST00000340027.10 linkuse as main transcriptc.*135T>C 3_prime_UTR_variant 4/41 NM_147130.3 P2O14931-1
LST1ENST00000438075.7 linkuse as main transcript downstream_gene_variant 1 NM_205839.3 P1O00453-1

Frequencies

GnomAD3 genomes
AF:
0.0882
AC:
13423
AN:
152146
Hom.:
864
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0300
Gnomad AMI
AF:
0.0822
Gnomad AMR
AF:
0.179
Gnomad ASJ
AF:
0.247
Gnomad EAS
AF:
0.155
Gnomad SAS
AF:
0.134
Gnomad FIN
AF:
0.0555
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.0916
Gnomad OTH
AF:
0.0966
GnomAD4 exome
AF:
0.0928
AC:
81309
AN:
876580
Hom.:
4977
Cov.:
12
AF XY:
0.0958
AC XY:
41842
AN XY:
436990
show subpopulations
Gnomad4 AFR exome
AF:
0.0329
Gnomad4 AMR exome
AF:
0.208
Gnomad4 ASJ exome
AF:
0.229
Gnomad4 EAS exome
AF:
0.198
Gnomad4 SAS exome
AF:
0.138
Gnomad4 FIN exome
AF:
0.0553
Gnomad4 NFE exome
AF:
0.0807
Gnomad4 OTH exome
AF:
0.100
GnomAD4 genome
AF:
0.0883
AC:
13445
AN:
152264
Hom.:
867
Cov.:
32
AF XY:
0.0905
AC XY:
6738
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0299
Gnomad4 AMR
AF:
0.179
Gnomad4 ASJ
AF:
0.247
Gnomad4 EAS
AF:
0.155
Gnomad4 SAS
AF:
0.134
Gnomad4 FIN
AF:
0.0555
Gnomad4 NFE
AF:
0.0916
Gnomad4 OTH
AF:
0.102
Alfa
AF:
0.0948
Hom.:
726
Bravo
AF:
0.0940
Asia WGS
AF:
0.132
AC:
460
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
7.3
DANN
Benign
0.59

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.

Other links and lift over

dbSNP: rs986475; hg19: chr6-31556709; API