rs3915568

Variant names:

• chr20-62738120-T-C
• rs3915568
• NM_002531.3:c.715-16565T>C

Variant summary

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

The NM_002531.3(NTSR1):​c.715-16565T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 108,788 control chromosomes in the GnomAD database, including 1,922 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 0.19 (1922 hom., cov: 29)
• Consequence: NTSR1 NM_002531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 11 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTSR1	NM_002531.3	c.715-16565T>C		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.715-16565T>C		intron_variant	Intron 1 of 3	1	NM_002531.3	ENSP00000359532.3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 21110 AN: 108724 Hom.: 1911 Cov.: 29

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.286

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.194 AC: 21142 AN: 108788 Hom.: 1922 Cov.: 29 AF XY: 0.201 AC XY: 10812 AN XY: 53670

African (AFR) AF: 0.114 AC: 1463 AN: 12782

American (AMR) AF: 0.286 AC: 3233 AN: 11304

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1159 AN: 3326

East Asian (EAS) AF: 0.276 AC: 806 AN: 2924

South Asian (SAS) AF: 0.189 AC: 777 AN: 4122

European-Finnish (FIN) AF: 0.257 AC: 2575 AN: 10010

Middle Eastern (MID) AF: 0.279 AC: 72 AN: 258

European-Non Finnish (NFE) AF: 0.172 AC: 10592 AN: 61684

Other (OTH) AF: 0.228 AC: 362 AN: 1588

Alfa AF: 0.163 Hom.: 3838

Bravo AF: 0.131

Asia WGS AF: 0.173 AC: 596 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.15
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: rs3915568; hg19: chr20-61369472;