Variant chr15-65003167-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_139242.4(MTFMT):c.1065G>A(p.Gln355Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0288 in 1,613,556 control chromosomes in the GnomAD database, including 1,344 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.028 ( 108 hom., cov: 31)

Exomes 𝑓: 0.029 ( 1236 hom. )

Consequence

MTFMT
NM_139242.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.113

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 15-65003167-C-T is Benign according to our data. Variant chr15-65003167-C-T is described in ClinVar as [Benign]. Clinvar id is 138266.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.113 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTFMT	NM_139242.4 link	c.1065G>A	p.Gln355Gln	synonymous_variant	9/9	ENST00000220058.9	NP_640335.2	Q96DP5-1
MTFMT	XM_005254158.6 link	c.1218G>A	p.Gln406Gln	synonymous_variant	9/9		XP_005254215.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MTFMT	ENST00000220058.9 link	c.1065G>A	p.Gln355Gln	synonymous_variant	9/9	1	NM_139242.4	ENSP00000220058.4	Q96DP5-1
MTFMT	ENST00000558460.5 link	n.1065G>A		non_coding_transcript_exon_variant	9/10	5		ENSP00000452646.1	Q96DP5-1
MTFMT	ENST00000560717.5 link	n.*535G>A		non_coding_transcript_exon_variant	8/8	5		ENSP00000457257.1	H3BTN9
MTFMT	ENST00000560717.5 link	n.*535G>A		3_prime_UTR_variant	8/8	5		ENSP00000457257.1	H3BTN9

Frequencies

GnomAD3 genomes

AF:

0.0276

AC:

4195

AN:

152016

Hom.:

108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0221

Gnomad AMI

AF:

0.0363

Gnomad AMR

AF:

0.0270

Gnomad ASJ

AF:

0.0603

Gnomad EAS

AF:

0.00829

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.0360

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0221

Gnomad OTH

AF:

0.0297

GnomAD3 exomes

AF:

0.0369

AC:

9178

AN:

248984

Hom.:

394

AF XY:

0.0424

AC XY:

5731

AN XY:

135094

show subpopulations

Gnomad AFR exome

AF:

0.0221

Gnomad AMR exome

AF:

0.0179

Gnomad ASJ exome

AF:

0.0628

Gnomad EAS exome

AF:

0.00390

Gnomad SAS exome

AF:

0.130

Gnomad FIN exome

AF:

0.0300

Gnomad NFE exome

AF:

0.0239

Gnomad OTH exome

AF:

0.0341

GnomAD4 exome

AF:

0.0289

AC:

42221

AN:

1461422

Hom.:

1236

Cov.:

AF XY:

0.0321

AC XY:

23349

AN XY:

726984

show subpopulations

Gnomad4 AFR exome

AF:

0.0223

Gnomad4 AMR exome

AF:

0.0181

Gnomad4 ASJ exome

AF:

0.0631

Gnomad4 EAS exome

AF:

0.00262

Gnomad4 SAS exome

AF:

0.126

Gnomad4 FIN exome

AF:

0.0276

Gnomad4 NFE exome

AF:

0.0219

Gnomad4 OTH exome

AF:

0.0327

GnomAD4 genome

AF:

0.0276

AC:

4199

AN:

152134

Hom.:

108

Cov.:

AF XY:

0.0304

AC XY:

2258

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.0221

Gnomad4 AMR

AF:

0.0268

Gnomad4 ASJ

AF:

0.0603

Gnomad4 EAS

AF:

0.00831

Gnomad4 SAS

AF:

0.131

Gnomad4 FIN

AF:

0.0360

Gnomad4 NFE

AF:

0.0221

Gnomad4 OTH

AF:

0.0299

Alfa

AF:

0.0252

Hom.:

Bravo

AF:

0.0235

Asia WGS

AF:

0.0660

AC:

229

AN:

3478

EpiCase

AF:

0.0235

EpiControl

AF:

0.0240

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 26, 2016	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 09, 2013

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

4.8

DANN

Benign

0.57

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