rs7038866

Positions:

• chr9-84772992-A-G
• chr9-84772992-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006180.6(NTRK2):​c.1396+20907A>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 152,120 control chromosomes in the GnomAD database, including 34,691 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 (34691 hom., cov: 32)
• Consequence: NTRK2 NM_006180.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTRK2	NM_006180.6	c.1396+20907A>G		intron_variant		ENST00000277120.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTRK2	ENST00000277120.8	c.1396+20907A>G		intron_variant		1	NM_006180.6	P3

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101888 AN: 152000 Hom.: 34688 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.776

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: 101938 AN: 152120 Hom.: 34691 Cov.: 32 AF XY: 0.674 AC XY: 50156 AN XY: 74364

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.670

Alfa AF: 0.689 Hom.: 6160

Bravo AF: 0.658

Asia WGS AF: 0.693 AC: 2407 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.70

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

Other links and lift over

dbSNP: rs7038866; hg19: chr9-87387907; COSMIC: COSV99451919;