rs3787521

Positions:

• chr20-62753374-T-C

Variant summary

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

The NM_002531.3(NTSR1):​c.715-1311T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.088 in 152,248 control chromosomes in the GnomAD database, including 748 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 0.088 (748 hom., cov: 33)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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 (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTSR1	NM_002531.3	c.715-1311T>C		intron_variant		ENST00000370501.4	NP_002522.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NTSR1	ENST00000370501.4	c.715-1311T>C		intron_variant		1	NM_002531.3	ENSP00000359532	P1

Frequencies

GnomAD3 genomes AF: 0.0879 AC: 13378 AN: 152130 Hom.: 746 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.0880 AC: 13397 AN: 152248 Hom.: 748 Cov.: 33 AF XY: 0.0863 AC XY: 6421 AN XY: 74436

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.0510

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.0606

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0512

Gnomad4 NFE AF: 0.0607

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0729 Hom.: 97

Bravo AF: 0.0889

Asia WGS AF: 0.0750 AC: 260 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	0.87
DANN	Benign	0.73

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: rs3787521; hg19: chr20-61384726;