rs1800832
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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
NM_006183.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0850
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]
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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=-0.67).
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 |
---|---|---|---|---|---|---|---|
NTS | NM_006183.5 | c.-3A>G | 5_prime_UTR_variant | 1/4 | ENST00000256010.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTS | ENST00000256010.7 | c.-3A>G | 5_prime_UTR_variant | 1/4 | 1 | NM_006183.5 | P1 | ||
NTS | ENST00000551529.5 | c.-3A>G | 5_prime_UTR_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0760 AC: 11566AN: 152098Hom.: 606 Cov.: 32
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GnomAD3 exomes AF: 0.0815 AC: 20486AN: 251238Hom.: 1163 AF XY: 0.0846 AC XY: 11488AN XY: 135784
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GnomAD4 exome AF: 0.0968 AC: 141109AN: 1457752Hom.: 7737 Cov.: 29 AF XY: 0.0966 AC XY: 70111AN XY: 725526
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GnomAD4 genome ? AF: 0.0760 AC: 11562AN: 152216Hom.: 605 Cov.: 32 AF XY: 0.0740 AC XY: 5510AN XY: 74410
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at