rs6011915

chr20-62728069-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002531.3(NTSR1):c.714+18148C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,086 control chromosomes in the GnomAD database, including 25,366 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 0.57 (25366 hom., cov: 33)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

NTSR1 (HGNC:8039): (neurotensin receptor 1) Neurotensin receptor 1 belongs to the large superfamily of G-protein coupled receptors. NTSR1 mediates the multiple functions of neurotensin, such as hypotension, hyperglycemia, hypothermia, antinociception, and regulation of intestinal motility and secretion. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTSR1	NM_002531.3	c.714+18148C>T		intron_variant		ENST00000370501.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTSR1	ENST00000370501.4	c.714+18148C>T		intron_variant		1	NM_002531.3	P1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86633 AN: 151968 Hom.: 25355 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.548

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.570 AC: 86678 AN: 152086 Hom.: 25366 Cov.: 33 AF XY: 0.564 AC XY: 41926 AN XY: 74352

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.548

Alfa AF: 0.614 Hom.: 33151

Bravo AF: 0.565

Asia WGS AF: 0.661 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.50

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

Other links and lift over

dbSNP: rs6011915; hg19: chr20-61359421; COSMIC: COSV65138288; COSMIC: COSV65138288;