20-62728621-G-A

Position:

• chr20-62728621-G-A

Variant summary

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

The NM_002531.3(NTSR1):​c.714+18700G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,158 control chromosomes in the GnomAD database, including 5,722 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 (5722 hom., cov: 33)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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=-0.91).
• 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/exons	MANE	Protein	UniProt
NTSR1	NM_002531.3	c.714+18700G>A		intron_variant		ENST00000370501.4	NP_002522.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NTSR1	ENST00000370501.4	c.714+18700G>A		intron_variant		1	NM_002531.3	ENSP00000359532.3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38777 AN: 152040 Hom.: 5712 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.255 AC: 38805 AN: 152158 Hom.: 5722 Cov.: 33 AF XY: 0.262 AC XY: 19470 AN XY: 74386

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.292

Alfa AF: 0.286 Hom.: 1166

Bravo AF: 0.250

Asia WGS AF: 0.237 AC: 826 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	0.24
DANN	Benign	0.66

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: rs2427422; hg19: chr20-61359973;