rs2249938

Positions:

• chr20-62756052-G-A
• chr20-62756052-G-C

Variant summary

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

The NM_002531.3(NTSR1):​c.916+1166G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 151,092 control chromosomes in the GnomAD database, including 46,123 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 0.77 (46123 hom., cov: 26)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTSR1	NM_002531.3	c.916+1166G>A		intron_variant		ENST00000370501.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTSR1	ENST00000370501.4	c.916+1166G>A		intron_variant		1	NM_002531.3	P1

Frequencies

GnomAD3 genomes AF: 0.768 AC: 115948 AN: 150972 Hom.: 46101 Cov.: 26

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.768 AC: 115996 AN: 151092 Hom.: 46123 Cov.: 26 AF XY: 0.768 AC XY: 56663 AN XY: 73764

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.787

Alfa AF: 0.854 Hom.: 85507

Bravo AF: 0.756

Asia WGS AF: 0.776 AC: 2701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.25
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2249938; hg19: chr20-61387404;