rs2004079

Variant names:

• chr15-35085064-T-C
• rs2004079
• NM_001355281.2:c.47A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-35085064-T-C
• chr15-35085064-T-G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001355281.2(NANOGP8):​c.47A>G​(p.Glu16Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 28)
• Consequence: NANOGP8 NM_001355281.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488
• Publications: 5 publications found

Genes affected

NANOGP8 (HGNC:23106): (Nanog homeobox retrogene P8) This gene represents a transcribed retrogene of the Nanog homeobox gene. The putative encoded protein may participate in reprogramming of cancer cells. In vitro studies using a recombinant protein have shown that the protein localizes to the nucleus and can promote cell proliferation, similar to the Nanog protein. [provided by RefSeq, Sep 2017]

LOC105370765 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08089298).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355281.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NANOGP8	NM_001355281.2	MANE Select	c.47A>G	p.Glu16Gly	missense	Exon 1 of 1	NP_001342210.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NANOGP8	ENST00000528386.4	TSL:6 MANE Select	c.47A>G	p.Glu16Gly	missense	Exon 1 of 1	ENSP00000487073.2

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.059
BayesDel_addAF	Benign	-0.47	T
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.6
DANN	Benign	0.38
FATHMM_MKL	Benign	0.0011	N
LIST_S2	Benign	0.36	T
MetaRNN	Benign	0.081	T
PhyloP100		-0.49
Sift4G	Benign	0.19	T
Vest4		0.053
MVP		0.13
GERP RS		1.9
PromoterAI		0.0033	Neutral
Varity_R		0.039
gMVP		0.23

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: rs2004079; hg19: chr15-35377265;