15-65002962-CAAAAAAAAAAA-CAAAAAAA

Variant names:

• chr15-65002962-CAAAA-C
• rs398027674
• NM_139242.4:c.*96_*99delTTTT

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_139242.4(MTFMT):​c.*96_*99delTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00285 in 324,572 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 0.000016 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0035 (0 hom.)
• Consequence: MTFMT NM_139242.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840

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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0035 (923/263808) while in subpopulation SAS AF= 0.00545 (55/10092). AF 95% confidence interval is 0.00449. There are 0 homozygotes in gnomad4_exome. There are 482 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTFMT	NM_139242.4	c.*96_*99delTTTT		3_prime_UTR_variant	Exon 9 of 9	ENST00000220058.9	NP_640335.2
MTFMT	XM_005254158.6	c.*96_*99delTTTT		3_prime_UTR_variant	Exon 9 of 9		XP_005254215.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTFMT	ENST00000220058	c.*96_*99delTTTT		3_prime_UTR_variant	Exon 9 of 9	1	NM_139242.4	ENSP00000220058.4
MTFMT	ENST00000558460.5	n.*96_*99delTTTT		non_coding_transcript_exon_variant	Exon 9 of 10	5		ENSP00000452646.1
MTFMT	ENST00000558460.5	n.*96_*99delTTTT		3_prime_UTR_variant	Exon 9 of 10	5		ENSP00000452646.1
MTFMT	ENST00000560717.5	n.*736_*739delTTTT		downstream_gene_variant		5		ENSP00000457257.1

Frequencies

GnomAD3 genomes AF: 0.0000165 AC: 1 AN: 60764 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000696

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: 0.00350 AC: 923 AN: 263808 Hom.: 0 AF XY: 0.00360 AC XY: 482 AN XY: 133894

Gnomad4 AFR exome AF: 0.00501

Gnomad4 AMR exome AF: 0.00530

Gnomad4 ASJ exome AF: 0.00411

Gnomad4 EAS exome AF: 0.00543

Gnomad4 SAS exome AF: 0.00545

Gnomad4 FIN exome AF: 0.00394

Gnomad4 NFE exome AF: 0.00311

Gnomad4 OTH exome AF: 0.00328

GnomAD4 genome AF: 0.0000165 AC: 1 AN: 60764 Hom.: 0 Cov.: 0 AF XY: 0.0000364 AC XY: 1 AN XY: 27452

Gnomad4 AFR AF: 0.0000696

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

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;