7-91880237-T-C

Variant names:

• chr7-91880237-T-C
• rs2269811
• ENST00000425936.1:c.-214A>G

Variant summary

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

The ENST00000425936.1(MTERF1):​c.-214A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 697,620 control chromosomes in the GnomAD database, including 7,020 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 0.14 (1731 hom., cov: 32)
  • Exomes 𝑓: 0.12 (5289 hom.)
• Consequence: MTERF1 ENST00000425936.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 12 publications found

Genes affected

MTERF1 (HGNC:21463): (mitochondrial transcription termination factor 1) This gene encodes a mitochondrial transcription termination factor. This protein participates in attenuating transcription from the mitochondrial genome; this attenuation allows higher levels of expression of 16S ribosomal RNA relative to the tRNA gene downstream. The product of this gene has three leucine zipper motifs bracketed by two basic domains that are all required for DNA binding. There is evidence that, for this protein, the zippers participate in intramolecular interactions that establish the three-dimensional structure required for DNA binding. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425936.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTERF1	NM_006980.5	MANE Select	c.-30-124A>G		intron	N/A	NP_008911.1	Q99551
	MTERF1	NM_001301134.2		c.-32+420A>G		intron	N/A	NP_001288063.1	B4DPR9
	MTERF1	NM_001301135.2		c.-191-124A>G		intron	N/A	NP_001288064.1	B4DPR9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTERF1	ENST00000425936.1	TSL:1	c.-214A>G		5_prime_UTR	Exon 1 of 2	ENSP00000400966.1	C9JU79
	MTERF1	ENST00000351870.8	TSL:1 MANE Select	c.-30-124A>G		intron	N/A	ENSP00000248643.3	Q99551
	MTERF1	ENST00000419292.1	TSL:1	c.-32+420A>G		intron	N/A	ENSP00000414116.1	B4DPR9

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21342 AN: 152098 Hom.: 1722 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.123 AC: 67120 AN: 545404 Hom.: 5289 Cov.: 7 AF XY: 0.123 AC XY: 35329 AN XY: 286860

African (AFR) AF: 0.195 AC: 2790 AN: 14302

American (AMR) AF: 0.115 AC: 2216 AN: 19262

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 1513 AN: 14712

East Asian (EAS) AF: 0.344 AC: 10924 AN: 31772

South Asian (SAS) AF: 0.134 AC: 6417 AN: 48052

European-Finnish (FIN) AF: 0.0970 AC: 3097 AN: 31936

Middle Eastern (MID) AF: 0.122 AC: 369 AN: 3028

European-Non Finnish (NFE) AF: 0.102 AC: 36154 AN: 353086

Other (OTH) AF: 0.124 AC: 3640 AN: 29254

GnomAD4 genome AF: 0.140 AC: 21373 AN: 152216 Hom.: 1731 Cov.: 32 AF XY: 0.141 AC XY: 10529 AN XY: 74412

African (AFR) AF: 0.196 AC: 8153 AN: 41516

American (AMR) AF: 0.114 AC: 1743 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1917 AN: 5180

South Asian (SAS) AF: 0.142 AC: 683 AN: 4824

European-Finnish (FIN) AF: 0.0951 AC: 1008 AN: 10596

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7078 AN: 68016

Other (OTH) AF: 0.128 AC: 270 AN: 2114

Alfa AF: 0.115 Hom.: 3246

Bravo AF: 0.146

Asia WGS AF: 0.213 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.49
PhyloP100		-1.5
PromoterAI		0.083	Neutral
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: rs2269811; hg19: chr7-91509551;