rs11063679

Positions:

• chr12-5442960-A-C
• chr12-5442960-A-T

Variant summary

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

The NM_001102654.2(NTF3):​c.18+10618A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0974 in 152,176 control chromosomes in the GnomAD database, including 855 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 0.097 (855 hom., cov: 32)
• Consequence: NTF3 NM_001102654.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.16

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTF3	NM_001102654.2	c.18+10618A>C		intron_variant		ENST00000423158.4	NP_001096124.1
NTF3	XM_011520963.3	c.-22+9628A>C		intron_variant			XP_011519265.1
NTF3	XM_047428901.1	c.-22+11767A>C		intron_variant			XP_047284857.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NTF3	ENST00000423158.4	c.18+10618A>C		intron_variant		1	NM_001102654.2	ENSP00000397297	P4
NTF3	ENST00000535299.5	n.231+10618A>C		intron_variant, non_coding_transcript_variant		5
NTF3	ENST00000543548.1	n.208+9628A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0974 AC: 14804 AN: 152058 Hom.: 853 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0764

Gnomad OTH AF: 0.0932

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

GnomAD4 genome AF: 0.0974 AC: 14822 AN: 152176 Hom.: 855 Cov.: 32 AF XY: 0.0958 AC XY: 7127 AN XY: 74406

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0768

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0762

Gnomad4 FIN AF: 0.0817

Gnomad4 NFE AF: 0.0764

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.0797 Hom.: 762

Bravo AF: 0.0995

Asia WGS AF: 0.0430 AC: 149 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	0.012
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11063679; hg19: chr12-5552126;