15-65002962-CA-C

Position:

• chr15-65002962-CA-C

Variant summary

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

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

• Frequency:
  • Genomes: 𝑓 0.016 (5 hom., cov: 0)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: MTFMT NM_139242.4 3_prime_UTR
• Clinical Significance: Likely 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-CA-C is Benign according to our data. Variant chr15-65002962-CA-C is described in ClinVar as [Likely_benign]. Clinvar id is 1205642.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTFMT	NM_139242.4	c.*99delT		3_prime_UTR_variant	9/9	ENST00000220058.9	NP_640335.2
MTFMT	XM_005254158.6	c.*99delT		3_prime_UTR_variant	9/9		XP_005254215.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTFMT	ENST00000220058	c.*99delT		3_prime_UTR_variant	9/9	1	NM_139242.4	ENSP00000220058.4
MTFMT	ENST00000558460.5	n.*99delT		non_coding_transcript_exon_variant	9/10	5		ENSP00000452646.1
MTFMT	ENST00000558460.5	n.*99delT		3_prime_UTR_variant	9/10	5		ENSP00000452646.1
MTFMT	ENST00000560717.5	n.*739delT		downstream_gene_variant		5		ENSP00000457257.1

Frequencies

GnomAD3 genomes AF: 0.0159 AC: 963 AN: 60738 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.0878

Gnomad AMR AF: 0.0193

Gnomad ASJ AF: 0.00221

Gnomad EAS AF: 0.00490

Gnomad SAS AF: 0.00696

Gnomad FIN AF: 0.00334

Gnomad MID AF: 0.0185

Gnomad NFE AF: 0.00737

Gnomad OTH AF: 0.0158

GnomAD4 exome AF: 0.104 AC: 27229 AN: 262120 Hom.: 0 Cov.: 2 AF XY: 0.104 AC XY: 13796 AN XY: 133020

Gnomad4 AFR exome AF: 0.136

Gnomad4 AMR exome AF: 0.120

Gnomad4 ASJ exome AF: 0.0999

Gnomad4 EAS exome AF: 0.156

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.0991

Gnomad4 NFE exome AF: 0.0982

Gnomad4 OTH exome AF: 0.107

GnomAD4 genome AF: 0.0160 AC: 972 AN: 60720 Hom.: 5 Cov.: 0 AF XY: 0.0167 AC XY: 459 AN XY: 27448

Gnomad4 AFR AF: 0.0376

Gnomad4 AMR AF: 0.0193

Gnomad4 ASJ AF: 0.00221

Gnomad4 EAS AF: 0.00492

Gnomad4 SAS AF: 0.00698

Gnomad4 FIN AF: 0.00334

Gnomad4 NFE AF: 0.00737

Gnomad4 OTH AF: 0.0157

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 13, 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;