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rs1573219

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006180.6(NTRK2):c.1396+20622A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,000 control chromosomes in the GnomAD database, including 34,677 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 0.67 ( 34677 hom., cov: 32)

Consequence

NTRK2
NM_006180.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.766
Variant links:
Genes affected
NTRK2 (HGNC:8032): (neurotrophic receptor tyrosine kinase 2) This gene encodes a member of the neurotrophic tyrosine receptor kinase (NTRK) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. Signalling through this kinase leads to cell differentiation. Mutations in this gene have been associated with obesity and mood disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NTRK2NM_006180.6 linkuse as main transcriptc.1396+20622A>G intron_variant ENST00000277120.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NTRK2ENST00000277120.8 linkuse as main transcriptc.1396+20622A>G intron_variant 1 NM_006180.6 P3Q16620-4

Frequencies

GnomAD3 genomes
AF:
0.670
AC:
101833
AN:
151882
Hom.:
34675
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.569
Gnomad AMI
AF:
0.718
Gnomad AMR
AF:
0.693
Gnomad ASJ
AF:
0.677
Gnomad EAS
AF:
0.739
Gnomad SAS
AF:
0.717
Gnomad FIN
AF:
0.777
Gnomad MID
AF:
0.604
Gnomad NFE
AF:
0.702
Gnomad OTH
AF:
0.670
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.670
AC:
101881
AN:
152000
Hom.:
34677
Cov.:
32
AF XY:
0.675
AC XY:
50125
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.568
Gnomad4 AMR
AF:
0.693
Gnomad4 ASJ
AF:
0.677
Gnomad4 EAS
AF:
0.739
Gnomad4 SAS
AF:
0.716
Gnomad4 FIN
AF:
0.777
Gnomad4 NFE
AF:
0.702
Gnomad4 OTH
AF:
0.670
Alfa
AF:
0.693
Hom.:
68158
Bravo
AF:
0.658
Asia WGS
AF:
0.694
AC:
2410
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
0.82
Dann
Benign
0.75

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: rs1573219; hg19: chr9-87387622; COSMIC: COSV99451917; API