NM_024865.4:c.152-721G>T

Variant names:

• chr12-7792229-G-T
• rs11055784
• NM_024865.4:c.152-721G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024865.4(NANOG):​c.152-721G>T 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 152,010 control chromosomes in the GnomAD database, including 20,126 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 (20126 hom., cov: 33)
• Consequence: NANOG NM_024865.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• 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 rank	MANE	Protein	UniProt
NANOG	NM_024865.4	c.152-721G>T		intron_variant	Intron 1 of 3	ENST00000229307.9	NP_079141.2
NANOG	NM_001297698.2	c.152-721G>T		intron_variant	Intron 1 of 3		NP_001284627.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NANOG	ENST00000229307.9	c.152-721G>T		intron_variant	Intron 1 of 3	1	NM_024865.4	ENSP00000229307.4
NANOG	ENST00000526286.1	c.152-721G>T		intron_variant	Intron 1 of 3	1		ENSP00000435288.1
NANOG	ENST00000541267.5	c.80-721G>T		intron_variant	Intron 3 of 5	5		ENSP00000444434.1
NANOG	ENST00000526434.2	n.334-759G>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75131 AN: 151892 Hom.: 20125 Cov.: 33

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.495 AC: 75171 AN: 152010 Hom.: 20126 Cov.: 33 AF XY: 0.493 AC XY: 36643 AN XY: 74300

African (AFR) AF: 0.351 AC: 14554 AN: 41460

American (AMR) AF: 0.532 AC: 8109 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3468

East Asian (EAS) AF: 0.0474 AC: 245 AN: 5172

South Asian (SAS) AF: 0.507 AC: 2446 AN: 4824

European-Finnish (FIN) AF: 0.564 AC: 5951 AN: 10556

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.586 AC: 39799 AN: 67964

Other (OTH) AF: 0.505 AC: 1065 AN: 2110

Alfa AF: 0.560 Hom.: 31801

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	-1.0
CADD	Benign	0.50
DANN	Benign	0.61
PhyloP100		-0.42
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11055784; hg19: chr12-7944825;