rs3787535

Variant names:

• chr20-62722169-G-A
• rs3787535
• NM_002531.3:c.714+12248G>A

Variant summary

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

The NM_002531.3(NTSR1):​c.714+12248G>A 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 152,048 control chromosomes in the GnomAD database, including 5,790 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 (5790 hom., cov: 32)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 10 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTSR1	NM_002531.3	c.714+12248G>A		intron_variant	Intron 1 of 3	ENST00000370501.4	NP_002522.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTSR1	ENST00000370501.4	c.714+12248G>A		intron_variant	Intron 1 of 3	1	NM_002531.3	ENSP00000359532.3

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39800 AN: 151930 Hom.: 5781 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: 0.214

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.351

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: 39830 AN: 152048 Hom.: 5790 Cov.: 32 AF XY: 0.267 AC XY: 19868 AN XY: 74310

African (AFR) AF: 0.153 AC: 6350 AN: 41470

American (AMR) AF: 0.351 AC: 5355 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1110 AN: 5178

South Asian (SAS) AF: 0.221 AC: 1066 AN: 4814

European-Finnish (FIN) AF: 0.355 AC: 3748 AN: 10558

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19802 AN: 67960

Other (OTH) AF: 0.289 AC: 611 AN: 2114

Alfa AF: 0.293 Hom.: 5531

Bravo AF: 0.261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.71
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: rs3787535; hg19: chr20-61353521;