rs10901140

Positions:

• chr9-132234647-G-A

Variant summary

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

The NM_032536.4(NTNG2):​c.1054+4052G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,240 control chromosomes in the GnomAD database, including 3,407 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 0.19 (3407 hom., cov: 34)
• Consequence: NTNG2 NM_032536.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

Genes affected

NTNG2 (HGNC:14288): (netrin G2) Predicted to be involved in several processes, including basement membrane assembly; cell morphogenesis involved in differentiation; and regulation of cell projection organization. Located in Flemming body; intercellular bridge; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTNG2	NM_032536.4	c.1054+4052G>A		intron_variant		ENST00000393229.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTNG2	ENST00000393229.4	c.1054+4052G>A		intron_variant		1	NM_032536.4	P1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29283 AN: 152122 Hom.: 3408 Cov.: 34

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.192 AC: 29302 AN: 152240 Hom.: 3407 Cov.: 34 AF XY: 0.198 AC XY: 14750 AN XY: 74410

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.205

Alfa AF: 0.180 Hom.: 2792

Bravo AF: 0.203

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.67

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: rs10901140; hg19: chr9-135110034;