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GeneBe

20-62709342-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_002531.3(NTSR1):c.135C>T(p.Arg45=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,609,706 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0074 ( 15 hom., cov: 33)
Exomes 𝑓: 0.00080 ( 19 hom. )

Consequence

NTSR1
NM_002531.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.35
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 20-62709342-C-T is Benign according to our data. Variant chr20-62709342-C-T is described in ClinVar as [Benign]. Clinvar id is 791213.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.35 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00738 (1125/152354) while in subpopulation AFR AF= 0.0256 (1064/41578). AF 95% confidence interval is 0.0243. There are 15 homozygotes in gnomad4. There are 532 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 15 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NTSR1NM_002531.3 linkuse as main transcriptc.135C>T p.Arg45= synonymous_variant 1/4 ENST00000370501.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NTSR1ENST00000370501.4 linkuse as main transcriptc.135C>T p.Arg45= synonymous_variant 1/41 NM_002531.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00739
AC:
1125
AN:
152238
Hom.:
15
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0257
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00430
GnomAD3 exomes
AF:
0.00210
AC:
509
AN:
242184
Hom.:
9
AF XY:
0.00167
AC XY:
220
AN XY:
132010
show subpopulations
Gnomad AFR exome
AF:
0.0259
Gnomad AMR exome
AF:
0.00222
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000660
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000167
Gnomad OTH exome
AF:
0.00134
GnomAD4 exome
AF:
0.000797
AC:
1162
AN:
1457352
Hom.:
19
Cov.:
32
AF XY:
0.000689
AC XY:
499
AN XY:
724576
show subpopulations
Gnomad4 AFR exome
AF:
0.0257
Gnomad4 AMR exome
AF:
0.00222
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000697
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000847
Gnomad4 OTH exome
AF:
0.00155
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00738
AC:
1125
AN:
152354
Hom.:
15
Cov.:
33
AF XY:
0.00714
AC XY:
532
AN XY:
74508
show subpopulations
Gnomad4 AFR
AF:
0.0256
Gnomad4 AMR
AF:
0.00261
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00425
Alfa
AF:
0.00312
Hom.:
2
Bravo
AF:
0.00865
Asia WGS
AF:
0.00173
AC:
7
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeApr 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
3.6
Dann
Benign
0.89

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61742231; hg19: chr20-61340694; API