chr1-93133724-A-C

Position:

• chr1-93133724-A-C

Variant summary

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

The NM_007358.4(MTF2):​c.1182A>C​(p.Glu394Asp) 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. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MTF2 NM_007358.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

Genes affected

MTF2 (HGNC:29535): (metal response element binding transcription factor 2) Enables methylated histone binding activity and transcription corepressor binding activity. Predicted to be involved in several processes, including regulation of histone H3-K27 methylation; regulation of transcription by RNA polymerase II; and segment specification. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Located in cytoplasm; focal adhesion; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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=0.07119554).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTF2	NM_007358.4	c.1182A>C	p.Glu394Asp	missense_variant	12/15	ENST00000370298.9
MTF2	NM_001164392.2	c.1011A>C	p.Glu337Asp	missense_variant	11/14
MTF2	NM_001164391.2	c.876A>C	p.Glu292Asp	missense_variant	13/16
MTF2	NM_001164393.2	c.876A>C	p.Glu292Asp	missense_variant	10/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTF2	ENST00000370298.9	c.1182A>C	p.Glu394Asp	missense_variant	12/15	1	NM_007358.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.095
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Benign	0.17	.;.;T;.
Eigen	Benign	-0.75
Eigen_PC	Benign	-0.58
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.77	.;T;T;T
M_CAP	Benign	0.0035	T
MetaRNN	Benign	0.071	T;T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.20	.;.;N;.
MutationTaster	Benign	0.82	D;D;D;D
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-0.83	N;N;N;N
REVEL	Benign	0.017
Sift	Benign	0.34	T;T;T;D
Sift4G	Benign	0.47	T;T;T;T
Polyphen		0.0020	.;.;B;.
Vest4		0.19
MutPred		0.13		.;.;Gain of loop (P = 0.0312);.;
MVP		0.30
MPC		0.26
ClinPred		0.22	T
GERP RS		1.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.044
gMVP		0.20

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-93599281;