rs223116

Variant names:

• chr14-23507801-A-G
• rs223116
• ENST00000703257.1:c.871-1539A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-23507801-A-G
• chr14-23507801-A-T

Variant summary

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

The ENST00000556699.2(NGDN):​c.929-1539A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,092 control chromosomes in the GnomAD database, including 29,798 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 0.58 (29798 hom., cov: 32)
• Consequence: NGDN ENST00000556699.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.738 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.871-1539A>G		intron_variant	Intron 9 of 9			ENSP00000515246.1
NGDN	ENST00000556699.2	c.929-1539A>G		intron_variant	Intron 10 of 10	2		ENSP00000451942.2

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88265 AN: 151974 Hom.: 29807 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.580 AC: 88262 AN: 152092 Hom.: 29798 Cov.: 32 AF XY: 0.587 AC XY: 43615 AN XY: 74334

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.601

Alfa AF: 0.720 Hom.: 82094

Bravo AF: 0.551

Asia WGS AF: 0.594 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223116; hg19: chr14-23977010;