20-62721825-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+11904C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,084 control chromosomes in the GnomAD database, including 5,789 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 0.26 (5789 hom., cov: 32)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

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 (AMR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTSR1	NM_002531.3	c.714+11904C>T		intron_variant		ENST00000370501.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTSR1	ENST00000370501.4	c.714+11904C>T		intron_variant		1	NM_002531.3	P1

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39815 AN: 151964 Hom.: 5779 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.262 AC: 39848 AN: 152084 Hom.: 5789 Cov.: 32 AF XY: 0.267 AC XY: 19873 AN XY: 74338

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.290

Alfa AF: 0.298 Hom.: 6864

Bravo AF: 0.261

Asia WGS AF: 0.244 AC: 852 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	5.3
Dann	Benign	0.60

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: rs4334545; hg19: chr20-61353177;