7-91815365-G-T

Variant names:

• chr7-91815365-G-T
• rs13229505
• ENST00000454222.5:n.159+12050C>A

Variant summary

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

The ENST00000454222.5(MTERF1):​n.159+12050C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,456 control chromosomes in the GnomAD database, including 9,064 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 (9064 hom., cov: 29)
• Consequence: MTERF1 ENST00000454222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 9 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=-0.97).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTERF1	ENST00000454222.5	n.159+12050C>A		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51505 AN: 151338 Hom.: 9061 Cov.: 29

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.377

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: 51534 AN: 151456 Hom.: 9064 Cov.: 29 AF XY: 0.338 AC XY: 24989 AN XY: 73960

African (AFR) AF: 0.284 AC: 11723 AN: 41306

American (AMR) AF: 0.330 AC: 5023 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1856 AN: 3470

East Asian (EAS) AF: 0.170 AC: 874 AN: 5150

South Asian (SAS) AF: 0.394 AC: 1871 AN: 4754

European-Finnish (FIN) AF: 0.335 AC: 3489 AN: 10418

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25570 AN: 67840

Other (OTH) AF: 0.375 AC: 791 AN: 2108

Alfa AF: 0.371 Hom.: 41203

Bravo AF: 0.337

Asia WGS AF: 0.298 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.63
DANN	Benign	0.17
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs13229505; hg19: chr7-91444679;