rs2815429

chr1-93125111-C-T

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTF2	NM_007358.4	c.922-2121C>T		intron_variant		ENST00000370298.9
MTF2	NM_001164391.2	c.616-2121C>T		intron_variant
MTF2	NM_001164392.2	c.922-2121C>T		intron_variant
MTF2	NM_001164393.2	c.616-2121C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTF2	ENST00000370298.9	c.922-2121C>T		intron_variant		1	NM_007358.4	P1

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

Gnomad4 AFR AF: 0.0483

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.0701

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.0783

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.127

Alfa AF: 0.113 Hom.: 836

Bravo AF: 0.112

Asia WGS AF: 0.211 AC: 731 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	8.1
Dann	Benign	0.72

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

LitVar

Other links and lift over

dbSNP: rs2815429; hg19: chr1-93590668;