20-62754435-A-G

Variant names:

• chr20-62754435-A-G
• rs856937
• NM_002531.3:c.715-250A>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.715-250A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,154 control chromosomes in the GnomAD database, including 53,643 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 0.84 (53643 hom., cov: 34)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTSR1	NM_002531.3	c.715-250A>G		intron_variant	Intron 1 of 3	ENST00000370501.4	NP_002522.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTSR1	ENST00000370501.4	c.715-250A>G		intron_variant	Intron 1 of 3	1	NM_002531.3	ENSP00000359532.3

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127352 AN: 152036 Hom.: 53605 Cov.: 34

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.838 AC: 127439 AN: 152154 Hom.: 53643 Cov.: 34 AF XY: 0.836 AC XY: 62170 AN XY: 74374

African (AFR) AF: 0.751 AC: 31143 AN: 41496

American (AMR) AF: 0.891 AC: 13644 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2989 AN: 3472

East Asian (EAS) AF: 0.921 AC: 4765 AN: 5172

South Asian (SAS) AF: 0.838 AC: 4039 AN: 4822

European-Finnish (FIN) AF: 0.820 AC: 8678 AN: 10588

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59335 AN: 67982

Other (OTH) AF: 0.854 AC: 1801 AN: 2110

Alfa AF: 0.863 Hom.: 92913

Bravo AF: 0.842

Asia WGS AF: 0.877 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.38
PhyloP100		0.26
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: rs856937; hg19: chr20-61385787;