rs2427427

Variant names:

• chr20-62732370-G-A
• rs2427427
• NM_002531.3:c.715-22315G>A

Variant summary

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

The NM_002531.3(NTSR1):​c.715-22315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,016 control chromosomes in the GnomAD database, including 8,847 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 0.34 (8847 hom., cov: 32)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 2 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]

NTSR1-AS1 (HGNC:40418):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTSR1	NM_002531.3	MANE Select	c.715-22315G>A		intron	N/A	NP_002522.2	P30989
	NTSR1-AS1	NR_199009.1		n.947C>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NTSR1	ENST00000370501.4	TSL:1 MANE Select	c.715-22315G>A		intron	N/A	ENSP00000359532.3	P30989
	NTSR1-AS1	ENST00000430184.1	TSL:3	n.*196C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50992 AN: 151898 Hom.: 8831 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.336 AC: 51042 AN: 152016 Hom.: 8847 Cov.: 32 AF XY: 0.341 AC XY: 25355 AN XY: 74312

African (AFR) AF: 0.349 AC: 14458 AN: 41442

American (AMR) AF: 0.388 AC: 5922 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1598 AN: 3468

East Asian (EAS) AF: 0.221 AC: 1146 AN: 5184

South Asian (SAS) AF: 0.300 AC: 1442 AN: 4810

European-Finnish (FIN) AF: 0.400 AC: 4231 AN: 10566

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21079 AN: 67972

Other (OTH) AF: 0.360 AC: 759 AN: 2108

Alfa AF: 0.332 Hom.: 2341

Bravo AF: 0.337

Asia WGS AF: 0.277 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.58
PhyloP100		0.36
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: rs2427427; hg19: chr20-61363722;