rs6950538

chr7-91788501-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000454222.5(MTERF1):n.159+38914A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,182 control chromosomes in the GnomAD database, including 9,153 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 0.34 (9153 hom., cov: 33)
• Consequence: MTERF1 ENST00000454222.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

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=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTERF1	ENST00000454222.5	n.159+38914A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51765 AN: 152064 Hom.: 9149 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.340 AC: 51796 AN: 152182 Hom.: 9153 Cov.: 33 AF XY: 0.338 AC XY: 25152 AN XY: 74404

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.376

Alfa AF: 0.377 Hom.: 6235

Bravo AF: 0.337

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	2.6
Dann	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6950538; hg19: chr7-91417816;