rs1800832

Variant names:

• chr12-85874401-A-G
• rs1800832
• NM_006183.5:c.-3A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-85874401-A-G
• chr12-85874401-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 16 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NTS	NM_006183.5	c.-3A>G		5_prime_UTR_variant	Exon 1 of 4	ENST00000256010.7	NP_006174.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTS	ENST00000256010.7	c.-3A>G		5_prime_UTR_variant	Exon 1 of 4	1	NM_006183.5	ENSP00000256010.5
NTS	ENST00000551529.5	c.-3A>G		5_prime_UTR_variant	Exon 1 of 3	3		ENSP00000448328.1

Frequencies

GnomAD3 genomes AF: 0.0760 AC: 11566 AN: 152098 Hom.: 606 Cov.: 32

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

GnomAD2 exomes AF: 0.0815 AC: 20486 AN: 251238 AF XY: 0.0846

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 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

African (AFR) AF: 0.0267 AC: 892 AN: 33426

American (AMR) AF: 0.0576 AC: 2577 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 4712 AN: 26066

East Asian (EAS) AF: 0.000151 AC: 6 AN: 39678

South Asian (SAS) AF: 0.0577 AC: 4973 AN: 86210

European-Finnish (FIN) AF: 0.0806 AC: 4302 AN: 53400

Middle Eastern (MID) AF: 0.182 AC: 1048 AN: 5750

European-Non Finnish (NFE) AF: 0.105 AC: 116590 AN: 1108296

Other (OTH) AF: 0.0998 AC: 6009 AN: 60208

GnomAD4 genome AF: 0.0760 AC: 11562 AN: 152216 Hom.: 605 Cov.: 32 AF XY: 0.0740 AC XY: 5510 AN XY: 74410

African (AFR) AF: 0.0260 AC: 1079 AN: 41558

American (AMR) AF: 0.0684 AC: 1046 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 682 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.0499 AC: 240 AN: 4812

European-Finnish (FIN) AF: 0.0786 AC: 834 AN: 10604

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7267 AN: 67998

Other (OTH) AF: 0.0927 AC: 196 AN: 2114

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
PhyloP100		0.085
PromoterAI		-0.050	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1800832; hg19: chr12-86268179;