rs9788972

Positions:

• chr17-9016313-G-A
• chr17-9016313-G-C

Variant summary

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

The XM_047437096.1(NTN1):​c.-63-5998G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,850 control chromosomes in the GnomAD database, including 6,336 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 0.29 (6336 hom., cov: 31)
• Consequence: NTN1 XM_047437096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

Genes affected

NTN1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTN1	XM_047437096.1	c.-63-5998G>A		intron_variant			XP_047293052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43378 AN: 151730 Hom.: 6334 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.286 AC: 43411 AN: 151850 Hom.: 6336 Cov.: 31 AF XY: 0.291 AC XY: 21564 AN XY: 74202

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.271

Alfa AF: 0.284 Hom.: 12578

Bravo AF: 0.283

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9788972; hg19: chr17-8919630;