rs7814319

Variant names:

• chr8-96251190-C-T
• rs7814319
• NM_015942.5:c.488-95G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015942.5. 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
	MTERF3	NM_015942.5	MANE Select	c.488-95G>A		intron	N/A	NP_057026.3
	MTERF3	NM_001286643.1		c.488-95G>A		intron	N/A	NP_001273572.1
	MTERF3	NM_001362964.1		c.-83-95G>A		intron	N/A	NP_001349893.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTERF3	ENST00000287025.4	TSL:1 MANE Select	c.488-95G>A		intron	N/A	ENSP00000287025.3
	MTERF3	ENST00000523821.5	TSL:1	c.488-95G>A		intron	N/A	ENSP00000429400.1
	MTERF3	ENST00000903462.1		c.530-95G>A		intron	N/A	ENSP00000573521.1

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

African (AFR) AF: 0.821 AC: 14067 AN: 17124

American (AMR) AF: 0.351 AC: 5530 AN: 15748

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 7691 AN: 15986

East Asian (EAS) AF: 0.308 AC: 9431 AN: 30638

South Asian (SAS) AF: 0.484 AC: 22887 AN: 47264

European-Finnish (FIN) AF: 0.477 AC: 16607 AN: 34808

Middle Eastern (MID) AF: 0.485 AC: 1488 AN: 3070

European-Non Finnish (NFE) AF: 0.480 AC: 293360 AN: 611134

Other (OTH) AF: 0.476 AC: 17893 AN: 37606

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

African (AFR) AF: 0.816 AC: 33881 AN: 41524

American (AMR) AF: 0.410 AC: 6264 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3470

East Asian (EAS) AF: 0.289 AC: 1491 AN: 5166

South Asian (SAS) AF: 0.456 AC: 2200 AN: 4824

European-Finnish (FIN) AF: 0.457 AC: 4831 AN: 10566

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32842 AN: 67962

Other (OTH) AF: 0.512 AC: 1081 AN: 2110

Alfa AF: 0.502 Hom.: 13858

Bravo AF: 0.561

Asia WGS AF: 0.397 AC: 1381 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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