chr7-91845693-A-G

Position:

• chr7-91845693-A-G

Variant summary

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

The ENST00000454222.5(MTERF1):​n.94-18213T>C 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 0.662 in 151,934 control chromosomes in the GnomAD database, including 33,711 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 0.66 (33711 hom., cov: 30)
• Consequence: MTERF1 ENST00000454222.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTERF1	ENST00000454222.5	n.94-18213T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100545 AN: 151816 Hom.: 33670 Cov.: 30

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.662 AC: 100644 AN: 151934 Hom.: 33711 Cov.: 30 AF XY: 0.665 AC XY: 49380 AN XY: 74274

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.627

Alfa AF: 0.616 Hom.: 40573

Bravo AF: 0.666

Asia WGS AF: 0.705 AC: 2450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9656002; hg19: chr7-91475007;