rs1894827

chr12-7790780-T-C

Variant summary

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

The NM_024865.4(NANOG):c.151+1015T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,998 control chromosomes in the GnomAD database, including 20,147 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 0.49 (20147 hom., cov: 31)
• Consequence: NANOG NM_024865.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.45

Genes affected

NANOG (HGNC:20857): (Nanog homeobox) The protein encoded by this gene is a DNA binding homeobox transcription factor involved in embryonic stem (ES) cell proliferation, renewal, and pluripotency. The encoded protein can block ES cell differentiation and can also autorepress its own expression in differentiating cells. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NANOG	NM_024865.4	c.151+1015T>C		intron_variant		ENST00000229307.9
NANOG	NM_001297698.2	c.151+1015T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NANOG	ENST00000229307.9	c.151+1015T>C		intron_variant		1	NM_024865.4	P1
NANOG	ENST00000526286.1	c.151+1015T>C		intron_variant		1
NANOG	ENST00000541267.5	c.79+1015T>C		intron_variant		5
NANOG	ENST00000526434.2	n.333+1015T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75172 AN: 151880 Hom.: 20146 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.0475

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.495 AC: 75212 AN: 151998 Hom.: 20147 Cov.: 31 AF XY: 0.493 AC XY: 36647 AN XY: 74274

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.0476

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.506

Alfa AF: 0.564 Hom.: 9202

Bravo AF: 0.481

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.5
Dann	Benign	0.18

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1894827; hg19: chr12-7943376;