chr8-96251190-C-T

Position:

• chr8-96251190-C-T

Variant summary

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

The NM_015942.5(MTERF3):​c.488-95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 965,494 control chromosomes in the GnomAD database, including 120,840 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 0.56 (25953 hom., cov: 32)
  • Exomes 𝑓: 0.48 (94887 hom.)
• Consequence: MTERF3 NM_015942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTERF3	NM_015942.5	c.488-95G>A		intron_variant		ENST00000287025.4	NP_057026.3
MTERF3	NM_001286643.1	c.488-95G>A		intron_variant			NP_001273572.1
MTERF3	NM_001362964.1	c.-83-95G>A		intron_variant			NP_001349893.1
MTERF3	XM_011517054.3	c.149-95G>A		intron_variant			XP_011515356.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTERF3	ENST00000287025.4	c.488-95G>A		intron_variant		1	NM_015942.5	ENSP00000287025.3
MTERF3	ENST00000523821.5	c.488-95G>A		intron_variant		1		ENSP00000429400.1
MTERF3	ENST00000522822.5	c.125-95G>A		intron_variant		2		ENSP00000430138.1
MTERF3	ENST00000524341.5	c.-83-95G>A		intron_variant		3		ENSP00000429267.1

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84874 AN: 151998 Hom.: 25903 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.516

GnomAD4 exome AF: 0.478 AC: 388954 AN: 813378 Hom.: 94887 AF XY: 0.478 AC XY: 197122 AN XY: 412212

Gnomad4 AFR exome AF: 0.821

Gnomad4 AMR exome AF: 0.351

Gnomad4 ASJ exome AF: 0.481

Gnomad4 EAS exome AF: 0.308

Gnomad4 SAS exome AF: 0.484

Gnomad4 FIN exome AF: 0.477

Gnomad4 NFE exome AF: 0.480

Gnomad4 OTH exome AF: 0.476

GnomAD4 genome AF: 0.559 AC: 84976 AN: 152116 Hom.: 25953 Cov.: 32 AF XY: 0.552 AC XY: 41077 AN XY: 74350

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.512

Alfa AF: 0.506 Hom.: 9498

Bravo AF: 0.561

Asia WGS AF: 0.397 AC: 1381 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7814319; hg19: chr8-97263418; COSMIC: COSV54632646;