rs2049314

Variant names:

• chr7-91834820-C-T
• rs2049314
• ENST00000454222.5:n.94-7340G>A

Variant summary

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

The ENST00000454222.5(MTERF1):​n.94-7340G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,058 control chromosomes in the GnomAD database, including 9,207 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 (9207 hom., cov: 32)
• Consequence: MTERF1 ENST00000454222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 4 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=-0.85).
• 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.94-7340G>A		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51904 AN: 151940 Hom.: 9206 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.341 AC: 51923 AN: 152058 Hom.: 9207 Cov.: 32 AF XY: 0.339 AC XY: 25190 AN XY: 74316

African (AFR) AF: 0.283 AC: 11759 AN: 41498

American (AMR) AF: 0.330 AC: 5049 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1869 AN: 3472

East Asian (EAS) AF: 0.169 AC: 873 AN: 5162

South Asian (SAS) AF: 0.394 AC: 1896 AN: 4818

European-Finnish (FIN) AF: 0.334 AC: 3527 AN: 10550

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

European-Non Finnish (NFE) AF: 0.380 AC: 25816 AN: 67962

Other (OTH) AF: 0.377 AC: 797 AN: 2112

Alfa AF: 0.380 Hom.: 9171

Bravo AF: 0.338

Asia WGS AF: 0.297 AC: 1032 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.099
DANN	Benign	0.76
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2049314; hg19: chr7-91464134;