14-23495210-C-T

Variant names:

• chr14-23495210-C-T
• rs7149201
• ENST00000703257.1:c.871-14130C>T

Variant summary

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

The ENST00000556699.2(NGDN):​c.929-14130C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,042 control chromosomes in the GnomAD database, including 36,908 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 0.69 (36908 hom., cov: 32)
• Consequence: NGDN ENST00000556699.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

Genes affected

NGDN (HGNC:20271): (neuroguidin) Neuroguidin is an EIF4E (MIM 133440)-binding protein that interacts with CPEB (MIM 607342) and functions as a translational regulatory protein during development of the vertebrate nervous system (Jung et al., 2006 [PubMed 16705177]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NGDN	ENST00000703257.1	c.871-14130C>T		intron_variant	Intron 9 of 9			ENSP00000515246.1
NGDN	ENST00000556699.2	c.929-14130C>T		intron_variant	Intron 10 of 10	2		ENSP00000451942.2

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104246 AN: 151924 Hom.: 36921 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.686 AC: 104243 AN: 152042 Hom.: 36908 Cov.: 32 AF XY: 0.690 AC XY: 51280 AN XY: 74336

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.708

Alfa AF: 0.750 Hom.: 54635

Bravo AF: 0.667

Asia WGS AF: 0.605 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7149201; hg19: chr14-23964419;