15-65002962-CAAAAAAAAAAA-CAAAAAAAA

Variant names:

• chr15-65002962-CAAA-C
• rs398027674
• NM_139242.4:c.*97_*99delTTT

Variant summary

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

The NM_139242.4(MTFMT):​c.*97_*99delTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 323,210 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 0.0022 (0 hom., cov: 0)
  • Exomes 𝑓: 0.012 (0 hom.)
• Consequence: MTFMT NM_139242.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

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 afr. gnomad4 allele frequency = 0.00222 (135/60738) while in subpopulation AFR AF= 0.0087 (125/14376). AF 95% confidence interval is 0.00746. There are 0 homozygotes in gnomad4. There are 66 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTFMT	NM_139242.4	c.*97_*99delTTT		3_prime_UTR_variant	Exon 9 of 9	ENST00000220058.9	NP_640335.2
MTFMT	XM_005254158.6	c.*97_*99delTTT		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.*97_*99delTTT		3_prime_UTR_variant	Exon 9 of 9	1	NM_139242.4	ENSP00000220058.4
MTFMT	ENST00000558460.5	n.*97_*99delTTT		non_coding_transcript_exon_variant	Exon 9 of 10	5		ENSP00000452646.1
MTFMT	ENST00000558460.5	n.*97_*99delTTT		3_prime_UTR_variant	Exon 9 of 10	5		ENSP00000452646.1
MTFMT	ENST00000560717.5	n.*737_*739delTTT		downstream_gene_variant		5		ENSP00000457257.1

Frequencies

GnomAD3 genomes AF: 0.00222 AC: 135 AN: 60756 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00870

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00159

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: 0.0000302

Gnomad OTH AF: 0.00132

GnomAD4 exome AF: 0.0123 AC: 3237 AN: 262472 Hom.: 0 AF XY: 0.0126 AC XY: 1681 AN XY: 133234

Gnomad4 AFR exome AF: 0.0174

Gnomad4 AMR exome AF: 0.0173

Gnomad4 ASJ exome AF: 0.0126

Gnomad4 EAS exome AF: 0.0185

Gnomad4 SAS exome AF: 0.0189

Gnomad4 FIN exome AF: 0.0122

Gnomad4 NFE exome AF: 0.0111

Gnomad4 OTH exome AF: 0.0137

GnomAD4 genome AF: 0.00222 AC: 135 AN: 60738 Hom.: 0 Cov.: 0 AF XY: 0.00240 AC XY: 66 AN XY: 27452

Gnomad4 AFR AF: 0.00870

Gnomad4 AMR AF: 0.00159

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000302

Gnomad4 OTH AF: 0.00131

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;