rs2815429

Variant names:

• chr1-93125111-C-T
• rs2815429
• NM_007358.4:c.922-2121C>T

Variant summary

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

The NM_007358.4(MTF2):​c.922-2121C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 151,728 control chromosomes in the GnomAD database, including 1,065 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 0.10 (1065 hom., cov: 31)
• Consequence: MTF2 NM_007358.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• Publications: 5 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007358.4. 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
	MTF2	NM_007358.4	MANE Select	c.922-2121C>T		intron	N/A	NP_031384.1
	MTF2	NM_001164392.2		c.922-2121C>T		intron	N/A	NP_001157864.1
	MTF2	NM_001164391.2		c.616-2121C>T		intron	N/A	NP_001157863.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTF2	ENST00000370298.9	TSL:1 MANE Select	c.922-2121C>T		intron	N/A	ENSP00000359321.4
	MTF2	ENST00000370303.4	TSL:1	c.922-2121C>T		intron	N/A	ENSP00000359326.4
	MTF2	ENST00000467953.5	TSL:1	n.905-2121C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15723 AN: 151610 Hom.: 1060 Cov.: 31

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0783

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.104 AC: 15739 AN: 151728 Hom.: 1065 Cov.: 31 AF XY: 0.107 AC XY: 7909 AN XY: 74134

African (AFR) AF: 0.0483 AC: 1999 AN: 41426

American (AMR) AF: 0.193 AC: 2945 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0701 AC: 243 AN: 3468

East Asian (EAS) AF: 0.282 AC: 1457 AN: 5160

South Asian (SAS) AF: 0.188 AC: 904 AN: 4810

European-Finnish (FIN) AF: 0.0783 AC: 825 AN: 10540

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 290

European-Non Finnish (NFE) AF: 0.102 AC: 6948 AN: 67788

Other (OTH) AF: 0.127 AC: 267 AN: 2104

Alfa AF: 0.111 Hom.: 944

Bravo AF: 0.112

Asia WGS AF: 0.211 AC: 731 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.1
DANN	Benign	0.72
PhyloP100		0.49
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: rs2815429; hg19: chr1-93590668;