Variant 15-65002962-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_139242.4(MTFMT):c.*99_*100insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.44 ( 7522 hom., cov: 0)

Exomes 𝑓: 0.27 ( 134 hom. )

Consequence

MTFMT
NM_139242.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.893

Variant links:

Genes affected

MTFMT (HGNC:29666): (mitochondrial methionyl-tRNA formyltransferase) The protein encoded by this nuclear gene localizes to the mitochondrion, where it catalyzes the formylation of methionyl-tRNA. [provided by RefSeq, Jun 2011]

MTFMT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 15-65002962-C-CA is Benign according to our data. Variant chr15-65002962-C-CA is described in ClinVar as [Benign]. Clinvar id is 1237194.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTFMT	NM_139242.4 linkuse as main transcript	c.99_100insT		3_prime_UTR_variant	9/9	ENST00000220058.9
MTFMT	XM_005254158.6 linkuse as main transcript	c.99_100insT		3_prime_UTR_variant	9/9

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTFMT	ENST00000220058.9 linkuse as main transcript	c.99_100insT	3_prime_UTR_variant	9/9	1	NM_139242.4	P1	Q96DP5-1
MTFMT	ENST00000558460.5 linkuse as main transcript	c.99_100insT	3_prime_UTR_variant, NMD_transcript_variant	9/10	5			Q96DP5-1
MTFMT	ENST00000560717.5 linkuse as main transcript		downstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.442

AC:

26939

AN:

60890

Hom.:

7523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.549

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.594

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.491

Gnomad FIN

AF:

0.376

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.425

GnomAD4 exome

AF:

0.273

AC:

71718

AN:

263134

Hom.:

134

Cov.:

AF XY:

0.272

AC XY:

36300

AN XY:

133580

show subpopulations

Gnomad4 AFR exome

AF:

0.202

Gnomad4 AMR exome

AF:

0.207

Gnomad4 ASJ exome

AF:

0.283

Gnomad4 EAS exome

AF:

0.188

Gnomad4 SAS exome

AF:

0.210

Gnomad4 FIN exome

AF:

0.262

Gnomad4 NFE exome

AF:

0.288

Gnomad4 OTH exome

AF:

0.267

GnomAD4 genome

AF:

0.442

AC:

26923

AN:

60872

Hom.:

7522

Cov.:

AF XY:

0.426

AC XY:

11727

AN XY:

27518

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.325

Gnomad4 ASJ

AF:

0.594

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.491

Gnomad4 FIN

AF:

0.376

Gnomad4 NFE

AF:

0.574

Gnomad4 OTH

AF:

0.424

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over