rs6089930

Positions:

• chr20-62727649-G-A
• chr20-62727649-G-T

Variant summary

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

The NM_002531.3(NTSR1):​c.714+17728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,178 control chromosomes in the GnomAD database, including 15,417 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 0.42 (15417 hom., cov: 33)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTSR1	NM_002531.3	c.714+17728G>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+17728G>A		intron_variant		1	NM_002531.3	ENSP00000359532	P1

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63415 AN: 152060 Hom.: 15416 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.417 AC: 63420 AN: 152178 Hom.: 15417 Cov.: 33 AF XY: 0.415 AC XY: 30858 AN XY: 74400

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.412

Alfa AF: 0.497 Hom.: 12871

Bravo AF: 0.405

Asia WGS AF: 0.582 AC: 2023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6089930; hg19: chr20-61359001;