15-65002962-CAAAAAAAAAAA-CAAAAAAAAAAAAA

Variant names:

• chr15-65002962-C-CAA
• rs398027674
• NM_139242.4:c.*98_*99dupTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_139242.4(MTFMT):​c.*98_*99dupTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.020 (70 hom., cov: 0)
  • Exomes 𝑓: 0.10 (1 hom.)
• Consequence: MTFMT NM_139242.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• 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 -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTFMT	NM_139242.4	c.*98_*99dupTT		3_prime_UTR_variant	Exon 9 of 9	ENST00000220058.9	NP_640335.2
MTFMT	XM_005254158.6	c.*98_*99dupTT		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.*98_*99dupTT		3_prime_UTR_variant	Exon 9 of 9	1	NM_139242.4	ENSP00000220058.4
MTFMT	ENST00000558460.5	n.*98_*99dupTT		non_coding_transcript_exon_variant	Exon 9 of 10	5		ENSP00000452646.1
MTFMT	ENST00000558460.5	n.*98_*99dupTT		3_prime_UTR_variant	Exon 9 of 10	5		ENSP00000452646.1
MTFMT	ENST00000560717.5	n.*738_*739dupTT		downstream_gene_variant		5		ENSP00000457257.1

Frequencies

GnomAD3 genomes AF: 0.0196 AC: 1172 AN: 59898 Hom.: 70 Cov.: 0

Gnomad AFR AF: 0.0271

Gnomad AMI AF: 0.0665

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.00329

Gnomad SAS AF: 0.00699

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0192

Gnomad NFE AF: 0.0173

Gnomad OTH AF: 0.0266

GnomAD4 exome AF: 0.102 AC: 26531 AN: 259696 Hom.: 1 Cov.: 2 AF XY: 0.102 AC XY: 13449 AN XY: 131774

Gnomad4 AFR exome AF: 0.0600

Gnomad4 AMR exome AF: 0.0812

Gnomad4 ASJ exome AF: 0.103

Gnomad4 EAS exome AF: 0.0418

Gnomad4 SAS exome AF: 0.0831

Gnomad4 FIN exome AF: 0.113

Gnomad4 NFE exome AF: 0.109

Gnomad4 OTH exome AF: 0.0980

GnomAD4 genome AF: 0.0196 AC: 1175 AN: 59880 Hom.: 70 Cov.: 0 AF XY: 0.0190 AC XY: 515 AN XY: 27090

Gnomad4 AFR AF: 0.0273

Gnomad4 AMR AF: 0.0157

Gnomad4 ASJ AF: 0.0158

Gnomad4 EAS AF: 0.00331

Gnomad4 SAS AF: 0.00702

Gnomad4 FIN AF: 0.0287

Gnomad4 NFE AF: 0.0173

Gnomad4 OTH AF: 0.0265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;