chr20-62727850-A-G

Variant names:

• chr20-62727850-A-G
• rs6011913
• NM_002531.3:c.714+17929A>G

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+17929A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,206 control chromosomes in the GnomAD database, including 46,042 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 0.76 (46042 hom., cov: 35)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.10
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002531.3. 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+17929A>G		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+17929A>G		intron	N/A	ENSP00000359532.3

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116029 AN: 152088 Hom.: 46018 Cov.: 35

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.763 AC: 116100 AN: 152206 Hom.: 46042 Cov.: 35 AF XY: 0.768 AC XY: 57166 AN XY: 74424

African (AFR) AF: 0.525 AC: 21803 AN: 41518

American (AMR) AF: 0.836 AC: 12794 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3031 AN: 3472

East Asian (EAS) AF: 0.962 AC: 4973 AN: 5170

South Asian (SAS) AF: 0.892 AC: 4309 AN: 4830

European-Finnish (FIN) AF: 0.868 AC: 9206 AN: 10604

Middle Eastern (MID) AF: 0.849 AC: 248 AN: 292

European-Non Finnish (NFE) AF: 0.842 AC: 57259 AN: 67984

Other (OTH) AF: 0.781 AC: 1652 AN: 2114

Alfa AF: 0.821 Hom.: 37351

Bravo AF: 0.752

Asia WGS AF: 0.904 AC: 3144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.76
DANN	Benign	0.27
PhyloP100		-4.1
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: rs6011913; hg19: chr20-61359202;