7-91880237-T-C

Position:

• chr7-91880237-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTERF1	NM_006980.5	c.-30-124A>G		intron_variant		ENST00000351870.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTERF1	ENST00000351870.8	c.-30-124A>G		intron_variant		1	NM_006980.5

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

Gnomad4 AFR exome AF: 0.195

Gnomad4 AMR exome AF: 0.115

Gnomad4 ASJ exome AF: 0.103

Gnomad4 EAS exome AF: 0.344

Gnomad4 SAS exome AF: 0.134

Gnomad4 FIN exome AF: 0.0970

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.124

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

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0951

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.128

Alfa AF: 0.113 Hom.: 2214

Bravo AF: 0.146

Asia WGS AF: 0.213 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.49

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: rs2269811; hg19: chr7-91509551;