Menu
GeneBe

rs1800832

Variant summary

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

The NM_006183.5(NTS):​c.-3A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0948 in 1,609,968 control chromosomes in the GnomAD database, including 8,342 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 0.076 ( 605 hom., cov: 32)
Exomes 𝑓: 0.097 ( 7737 hom. )

Consequence

NTS
NM_006183.5 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0850
Variant links:
Genes affected
NTS (HGNC:8038): (neurotensin) This gene encodes a common precursor for two peptides, neuromedin N and neurotensin. Neurotensin is a secreted tridecapeptide, which is widely distributed throughout the central nervous system, and may function as a neurotransmitter or a neuromodulator. It may be involved in dopamine-associated pathophysiological events, in the maintenance of gut structure and function, and in the regulation of fat metabolism. Neurotensin also exhibits antimicrobial activity against bacteria and fungi. Tissue-specific processing may lead to the formation in some tissues of larger forms of neuromedin N and neurotensin. The large forms may represent more stable peptides that are also biologically active. [provided by RefSeq, Oct 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NTSNM_006183.5 linkuse as main transcriptc.-3A>G 5_prime_UTR_variant 1/4 ENST00000256010.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NTSENST00000256010.7 linkuse as main transcriptc.-3A>G 5_prime_UTR_variant 1/41 NM_006183.5 P1
NTSENST00000551529.5 linkuse as main transcriptc.-3A>G 5_prime_UTR_variant 1/33

Frequencies

GnomAD3 genomes
AF:
0.0760
AC:
11566
AN:
152098
Hom.:
606
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0260
Gnomad AMI
AF:
0.170
Gnomad AMR
AF:
0.0685
Gnomad ASJ
AF:
0.197
Gnomad EAS
AF:
0.000579
Gnomad SAS
AF:
0.0500
Gnomad FIN
AF:
0.0786
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.107
Gnomad OTH
AF:
0.0937
GnomAD3 exomes
AF:
0.0815
AC:
20486
AN:
251238
Hom.:
1163
AF XY:
0.0846
AC XY:
11488
AN XY:
135784
show subpopulations
Gnomad AFR exome
AF:
0.0233
Gnomad AMR exome
AF:
0.0553
Gnomad ASJ exome
AF:
0.184
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0554
Gnomad FIN exome
AF:
0.0781
Gnomad NFE exome
AF:
0.108
Gnomad OTH exome
AF:
0.108
GnomAD4 exome
AF:
0.0968
AC:
141109
AN:
1457752
Hom.:
7737
Cov.:
29
AF XY:
0.0966
AC XY:
70111
AN XY:
725526
show subpopulations
Gnomad4 AFR exome
AF:
0.0267
Gnomad4 AMR exome
AF:
0.0576
Gnomad4 ASJ exome
AF:
0.181
Gnomad4 EAS exome
AF:
0.000151
Gnomad4 SAS exome
AF:
0.0577
Gnomad4 FIN exome
AF:
0.0806
Gnomad4 NFE exome
AF:
0.105
Gnomad4 OTH exome
AF:
0.0998
GnomAD4 genome
AF:
0.0760
AC:
11562
AN:
152216
Hom.:
605
Cov.:
32
AF XY:
0.0740
AC XY:
5510
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.0260
Gnomad4 AMR
AF:
0.0684
Gnomad4 ASJ
AF:
0.197
Gnomad4 EAS
AF:
0.000580
Gnomad4 SAS
AF:
0.0499
Gnomad4 FIN
AF:
0.0786
Gnomad4 NFE
AF:
0.107
Gnomad4 OTH
AF:
0.0927
Alfa
AF:
0.103
Hom.:
487
Bravo
AF:
0.0752
Asia WGS
AF:
0.0210
AC:
74
AN:
3478
EpiCase
AF:
0.118
EpiControl
AF:
0.118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
12
DANN
Benign
0.80

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: rs1800832; hg19: chr12-86268179; API