Genetic Variant MTFMT:c.*95_*99delTTTTT (chr15-65002962-CAAAAA-C) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_139242.4(MTFMT):c.*95_*99delTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000645 in 325,388 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000082 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00077 ( 0 hom. )

Consequence

MTFMT
NM_139242.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.840

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 Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTFMT	NM_139242.4 link	c.95_99delTTTTT		3_prime_UTR_variant	Exon 9 of 9	ENST00000220058.9	NP_640335.2	Q96DP5-1
MTFMT	XM_005254158.6 link	c.95_99delTTTTT		3_prime_UTR_variant	Exon 9 of 9		XP_005254215.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MTFMT	ENST00000220058 link	c.95_99delTTTTT	3_prime_UTR_variant	Exon 9 of 9	1	NM_139242.4	ENSP00000220058.4	Q96DP5-1
MTFMT	ENST00000558460.5 link	n.95_99delTTTTT	non_coding_transcript_exon_variant	Exon 9 of 10	5		ENSP00000452646.1	Q96DP5-1
MTFMT	ENST00000558460.5 link	n.95_99delTTTTT	3_prime_UTR_variant	Exon 9 of 10	5		ENSP00000452646.1	Q96DP5-1
MTFMT	ENST00000560717.5 link	n.735_739delTTTTT	downstream_gene_variant		5		ENSP00000457257.1	H3BTN9

Frequencies

GnomAD3 genomes

AF:

0.0000823

AC:

AN:

60766

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000348

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000775

AC:

205

AN:

264622

Hom.:

AF XY:

0.000752

AC XY:

101

AN XY:

134346

show subpopulations

Gnomad4 AFR exome

AF:

0.000604

Gnomad4 AMR exome

AF:

0.000852

Gnomad4 ASJ exome

AF:

0.00125

Gnomad4 EAS exome

AF:

0.00137

Gnomad4 SAS exome

AF:

0.00119

Gnomad4 FIN exome

AF:

0.000784

Gnomad4 NFE exome

AF:

0.000711

Gnomad4 OTH exome

AF:

0.000532

GnomAD4 genome

AF:

0.0000823

AC:

AN:

60766

Hom.:

Cov.:

AF XY:

0.000109

AC XY:

AN XY:

27454

show subpopulations

Gnomad4 AFR

AF:

0.000348

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

15-65002962-CAAAAAAAAAAA-CAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over