chr7-91845693-A-G

Variant names:

• chr7-91845693-A-G
• rs9656002
• ENST00000454222.5:n.94-18213T>C

Variant summary

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

The ENST00000454222.5(MTERF1):​n.94-18213T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454222.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTERF1	ENST00000454222.5	TSL:5	n.94-18213T>C		intron	N/A

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

African (AFR) AF: 0.731 AC: 30294 AN: 41444

American (AMR) AF: 0.672 AC: 10258 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1602 AN: 3470

East Asian (EAS) AF: 0.831 AC: 4275 AN: 5142

South Asian (SAS) AF: 0.605 AC: 2920 AN: 4824

European-Finnish (FIN) AF: 0.666 AC: 7032 AN: 10554

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42075 AN: 67932

Other (OTH) AF: 0.627 AC: 1321 AN: 2106

Alfa AF: 0.621 Hom.: 57677

Bravo AF: 0.666

Asia WGS AF: 0.705 AC: 2450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs9656002; hg19: chr7-91475007;