20-62728736-G-T

Variant names:

• chr20-62728736-G-T
• rs2427424
• NM_002531.3:c.714+18815G>T

Variant summary

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

The ENST00000370501.4(NTSR1):​c.714+18815G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,988 control chromosomes in the GnomAD database, including 5,779 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 (5779 hom., cov: 32)
• Consequence: NTSR1 ENST00000370501.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000370501.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTSR1	NM_002531.3	MANE Select	c.714+18815G>T		intron	N/A	NP_002522.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTSR1	ENST00000370501.4	TSL:1 MANE Select	c.714+18815G>T		intron	N/A	ENSP00000359532.3

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39195 AN: 151870 Hom.: 5769 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.258 AC: 39222 AN: 151988 Hom.: 5779 Cov.: 32 AF XY: 0.265 AC XY: 19677 AN XY: 74288

African (AFR) AF: 0.136 AC: 5645 AN: 41490

American (AMR) AF: 0.352 AC: 5371 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1487 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1157 AN: 5142

South Asian (SAS) AF: 0.224 AC: 1080 AN: 4816

European-Finnish (FIN) AF: 0.381 AC: 4019 AN: 10560

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.287 AC: 19498 AN: 67932

Other (OTH) AF: 0.294 AC: 620 AN: 2110

Alfa AF: 0.278 Hom.: 16200

Bravo AF: 0.253

Asia WGS AF: 0.238 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.43
PhyloP100		-0.29
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: rs2427424; hg19: chr20-61360088;