chr20-62728167-G-A

Variant names:

• chr20-62728167-G-A
• rs6010969
• NM_002531.3:c.714+18246G>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+18246G>A 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 152,028 control chromosomes in the GnomAD database, including 25,336 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 (25336 hom., cov: 33)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002531.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTSR1	NM_002531.3	MANE Select	c.714+18246G>A		intron	N/A	NP_002522.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTSR1	ENST00000370501.4	TSL:1 MANE Select	c.714+18246G>A		intron	N/A	ENSP00000359532.3

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86568 AN: 151912 Hom.: 25326 Cov.: 33

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.516

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: 86611 AN: 152028 Hom.: 25336 Cov.: 33 AF XY: 0.564 AC XY: 41904 AN XY: 74316

African (AFR) AF: 0.467 AC: 19337 AN: 41436

American (AMR) AF: 0.533 AC: 8148 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1810 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3899 AN: 5142

South Asian (SAS) AF: 0.671 AC: 3240 AN: 4828

European-Finnish (FIN) AF: 0.516 AC: 5467 AN: 10590

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

European-Non Finnish (NFE) AF: 0.630 AC: 42806 AN: 67948

Other (OTH) AF: 0.548 AC: 1155 AN: 2108

Alfa AF: 0.602 Hom.: 5598

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	-0.95
CADD	Benign	0.82
DANN	Benign	0.63
PhyloP100		-1.7
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: rs6010969; hg19: chr20-61359519; COSMIC: COSV65138292; COSMIC: COSV65138292;