20-62718738-T-C

Variant names:

• chr20-62718738-T-C
• rs6062460
• NM_002531.3:c.714+8817T>C

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+8817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,060 control chromosomes in the GnomAD database, including 35,962 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 0.66 (35962 hom., cov: 31)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTSR1	NM_002531.3	c.714+8817T>C		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+8817T>C		intron_variant	Intron 1 of 3	1	NM_002531.3	ENSP00000359532.3

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99966 AN: 151944 Hom.: 35950 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.658 AC: 99996 AN: 152060 Hom.: 35962 Cov.: 31 AF XY: 0.662 AC XY: 49211 AN XY: 74344

African (AFR) AF: 0.337 AC: 13958 AN: 41456

American (AMR) AF: 0.777 AC: 11881 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2809 AN: 3464

East Asian (EAS) AF: 0.937 AC: 4860 AN: 5186

South Asian (SAS) AF: 0.785 AC: 3783 AN: 4820

European-Finnish (FIN) AF: 0.738 AC: 7799 AN: 10570

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52446 AN: 67952

Other (OTH) AF: 0.691 AC: 1460 AN: 2112

Alfa AF: 0.751 Hom.: 28594

Bravo AF: 0.651

Asia WGS AF: 0.825 AC: 2868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.40
PhyloP100		-1.5
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: rs6062460; hg19: chr20-61350090;