rs6011899

Positions:

• chr20-62724905-T-C

Variant summary

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

The NM_002531.3(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 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTSR1	NM_002531.3	c.714+14984T>C		intron_variant		ENST00000370501.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTSR1	ENST00000370501.4	c.714+14984T>C		intron_variant		1	NM_002531.3	P1

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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0979

Gnomad4 EAS AF: 0.0380

Gnomad4 SAS AF: 0.0975

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.150

Alfa AF: 0.145 Hom.: 333

Bravo AF: 0.180

Asia WGS AF: 0.0970 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.41

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

Publications

LitVar

Other links and lift over

dbSNP: rs6011899; hg19: chr20-61356257;