chr15-65002962-C-CA

Position:

• chr15-65002962-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.893

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]

ACMG classification

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	c.*99_*100insT		3_prime_UTR_variant	9/9	ENST00000220058.9
MTFMT	XM_005254158.6	c.*99_*100insT		3_prime_UTR_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTFMT	ENST00000220058.9	c.*99_*100insT		3_prime_UTR_variant	9/9	1	NM_139242.4	P1
MTFMT	ENST00000558460.5	c.*99_*100insT		3_prime_UTR_variant, NMD_transcript_variant	9/10	5
MTFMT	ENST00000560717.5			downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.442 AC: 26939 AN: 60890 Hom.: 7523 Cov.: 0

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.: 2 AF XY: 0.272 AC XY: 36300 AN XY: 133580

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.: 0 AF XY: 0.426 AC XY: 11727 AN XY: 27518

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs398027674; hg19: chr15-65295300;