rs6011899

Variant names:

• chr20-62724905-T-C
• rs6011899
• NM_002531.3:c.714+14984T>C

Variant summary

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

The ENST00000370501.4(NTSR1):​c.714+14984T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,200 control chromosomes in the GnomAD database, including 3,444 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 0.17 (3444 hom., cov: 34)
• Consequence: NTSR1 ENST00000370501.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 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+14984T>C		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+14984T>C		intron	N/A	ENSP00000359532.3

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25912 AN: 152082 Hom.: 3434 Cov.: 34

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.171 AC: 25957 AN: 152200 Hom.: 3444 Cov.: 34 AF XY: 0.166 AC XY: 12320 AN XY: 74428

African (AFR) AF: 0.369 AC: 15301 AN: 41454

American (AMR) AF: 0.102 AC: 1555 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0979 AC: 340 AN: 3472

East Asian (EAS) AF: 0.0380 AC: 197 AN: 5184

South Asian (SAS) AF: 0.0975 AC: 471 AN: 4832

European-Finnish (FIN) AF: 0.0736 AC: 781 AN: 10614

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6869 AN: 68018

Other (OTH) AF: 0.150 AC: 317 AN: 2112

Alfa AF: 0.227 Hom.: 1262

Bravo AF: 0.180

Asia WGS AF: 0.0970 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.41
PhyloP100		-0.56
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: rs6011899; hg19: chr20-61356257;