rs6011915

Variant names:

• chr20-62728069-C-T
• rs6011915
• NM_002531.3:c.714+18148C>T

Variant summary

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

The ENST00000370501.4(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 ENST00000370501.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000370501.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTSR1	NM_002531.3	MANE Select	c.714+18148C>T		intron	N/A	NP_002522.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTSR1	ENST00000370501.4	TSL:1 MANE Select	c.714+18148C>T		intron	N/A	ENSP00000359532.3

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

African (AFR) AF: 0.468 AC: 19408 AN: 41476

American (AMR) AF: 0.533 AC: 8150 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1810 AN: 3468

East Asian (EAS) AF: 0.757 AC: 3886 AN: 5132

South Asian (SAS) AF: 0.671 AC: 3238 AN: 4826

European-Finnish (FIN) AF: 0.515 AC: 5450 AN: 10586

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42829 AN: 67982

Other (OTH) AF: 0.548 AC: 1158 AN: 2114

Alfa AF: 0.612 Hom.: 40387

Bravo AF: 0.565

Asia WGS AF: 0.661 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-1.6
Mutation Taster		=100/0	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: rs6011915; hg19: chr20-61359421; COSMIC: COSV65138288; COSMIC: COSV65138288;