rs11063714

chr12-5495767-G-A

Variant summary

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

The ENST00000535299.5(NTF3):n.232-10798G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 152,078 control chromosomes in the GnomAD database, including 976 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 0.060 (976 hom., cov: 33)
• Consequence: NTF3 ENST00000535299.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

Genes affected

NTF3 (HGNC:8023): (neurotrophin 3) The protein encoded by this gene is a member of the neurotrophin family, that controls survival and differentiation of mammalian neurons. This protein is closely related to both nerve growth factor and brain-derived neurotrophic factor. It may be involved in the maintenance of the adult nervous system, and may affect development of neurons in the embryo when it is expressed in human placenta. NTF3-deficient mice generated by gene targeting display severe movement defects of the limbs. The mature peptide of this protein is identical in all mammals examined including human, pig, rat and mouse. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTF3	ENST00000535299.5	n.232-10798G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 9128 AN: 151960 Hom.: 972 Cov.: 33

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.0566

Gnomad FIN AF: 0.0447

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00548

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0601 AC: 9145 AN: 152078 Hom.: 976 Cov.: 33 AF XY: 0.0651 AC XY: 4843 AN XY: 74354

Gnomad4 AFR AF: 0.0854

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.0560

Gnomad4 FIN AF: 0.0447

Gnomad4 NFE AF: 0.00549

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0217 Hom.: 217

Bravo AF: 0.0722

Asia WGS AF: 0.232 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.2
Dann	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11063714; hg19: chr12-5604933;