8-96261601-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_015942.5(MTERF3):c.-111G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0593 in 155,030 control chromosomes in the GnomAD database, including 833 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.060 (830 hom., cov: 33)
  • Exomes 𝑓: 0.011 (3 hom.)
• Consequence: MTERF3 NM_015942.5 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.84

Genes affected

MTERF3 (HGNC:24258): (mitochondrial transcription termination factor 3) Enables transcription cis-regulatory region binding activity. Involved in negative regulation of transcription, DNA-templated. Located in cytosol and mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 8-96261601-C-G is Benign according to our data. Variant chr8-96261601-C-G is described in ClinVar as [Benign]. Clinvar id is 1292007.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTERF3	NM_015942.5	c.-111G>C		5_prime_UTR_variant	1/8	ENST00000287025.4
MTERF3	NM_001286643.1	c.-111G>C		5_prime_UTR_variant	1/9
MTERF3	NM_001362964.1	c.-646G>C		5_prime_UTR_variant	1/8
MTERF3	XM_011517054.3	c.-580G>C		5_prime_UTR_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTERF3	ENST00000287025.4	c.-111G>C		5_prime_UTR_variant	1/8	1	NM_015942.5	P1
MTERF3	ENST00000523821.5	c.-111G>C		5_prime_UTR_variant	1/9	1
MTERF3	ENST00000517720.1			upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9125 AN: 152078 Hom.: 821 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.0324

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00163

Gnomad OTH AF: 0.0387

GnomAD4 exome AF: 0.0106 AC: 30 AN: 2838 Hom.: 3 Cov.: 0 AF XY: 0.0141 AC XY: 23 AN XY: 1634

Gnomad4 AFR exome AF: 0.275

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0435

Gnomad4 SAS exome AF: 0.0228

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000548

Gnomad4 OTH exome AF: 0.0152

GnomAD4 genome AF: 0.0602 AC: 9168 AN: 152192 Hom.: 830 Cov.: 33 AF XY: 0.0586 AC XY: 4361 AN XY: 74428

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.0231

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.0325

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00163

Gnomad4 OTH AF: 0.0383

Alfa AF: 0.00220 Hom.: 2

Bravo AF: 0.0660

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.96
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2280262; hg19: chr8-97273829;