rs2427422

Variant names:

• chr20-62728621-G-A
• rs2427422
• NM_002531.3:c.714+18700G>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+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
• Publications: 11 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 (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+18700G>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+18700G>A		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.127 AC: 5254 AN: 41522

American (AMR) AF: 0.351 AC: 5369 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1479 AN: 3462

East Asian (EAS) AF: 0.224 AC: 1160 AN: 5174

South Asian (SAS) AF: 0.220 AC: 1062 AN: 4826

European-Finnish (FIN) AF: 0.380 AC: 4019 AN: 10578

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19494 AN: 67986

Other (OTH) AF: 0.292 AC: 617 AN: 2112

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
PhyloP100		-1.2
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: rs2427422; hg19: chr20-61359973;