15-65002962-C-A

Position:

• chr15-65002962-C-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_139242.4(MTFMT):​c.*100G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.10 (0 hom., cov: 9)
  • Exomes 𝑓: 0.0000038 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTFMT NM_139242.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.07

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 Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 15-65002962-C-A is Benign according to our data. Variant chr15-65002962-C-A is described in ClinVar as [Benign]. Clinvar id is 1178547.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTFMT	NM_139242.4	c.*100G>T		3_prime_UTR_variant	9/9	ENST00000220058.9
MTFMT	XM_005254158.6	c.*100G>T		3_prime_UTR_variant	9/9

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 6099 AN: 58832 Hom.: 0 Cov.: 9 FAILED QC

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0585

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0747

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.0278

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.0949

GnomAD4 exome AF: 0.00000377 AC: 1 AN: 264998 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 134524

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000758

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.104 AC: 6100 AN: 58820 Hom.: 0 Cov.: 9 AF XY: 0.106 AC XY: 2825 AN XY: 26586

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0747

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.0880

Gnomad4 FIN AF: 0.0722

Gnomad4 NFE AF: 0.0757

Gnomad4 OTH AF: 0.0946

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

Jul 30, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.6
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs866953579; hg19: chr15-65295300;