rs372662189

Variant names:

• chr9-96931832-C-G
• rs372662189
• NM_001170741.3:c.127C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-96931832-C-G
• chr9-96931832-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001170741.3(NUTM2G):​c.127C>G​(p.Leu43Val) 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. 14/20 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: 30)
• Consequence: NUTM2G NM_001170741.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

NUTM2G (HGNC:23449): (NUT family member 2G)

ZNF782 (HGNC:33110): (zinc finger protein 782) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MFSD14CP (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09846488).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTM2G	NM_001170741.3	c.127C>G	p.Leu43Val	missense_variant	Exon 2 of 7	ENST00000372322.4	NP_001164212.1
NUTM2G	NM_001045477.4	c.127C>G	p.Leu43Val	missense_variant	Exon 2 of 7		NP_001038942.1
ZNF782	XM_047422874.1	c.-439+1952G>C		intron_variant	Intron 1 of 3		XP_047278830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUTM2G	ENST00000372322.4	c.127C>G	p.Leu43Val	missense_variant	Exon 2 of 7	5	NM_001170741.3	ENSP00000361397.3

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 30

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.2
DANN	Benign	0.90
DEOGEN2	Benign	0.059	.;T
Eigen	Benign	-0.63
Eigen_PC	Benign	-0.96
FATHMM_MKL	Benign	0.0074	N
LIST_S2	Benign	0.68	T;T
M_CAP	Benign	0.0013	T
MetaRNN	Benign	0.098	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.6	M;M
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-1.2	N;N
REVEL	Benign	0.044
Sift	Benign	0.13	T;T
Sift4G	Benign	0.51	T;T
Polyphen		1.0	D;.
Vest4		0.089
MutPred		0.28		Loss of sheet (P = 0.0054);Loss of sheet (P = 0.0054);
MVP		0.014
ClinPred		0.11	T
GERP RS		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.059
gMVP		0.054

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: rs372662189; hg19: chr9-99694114;