15-65002962-CAAAAAAAAAAA-CAAAAAAAAAAAAAA

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_139242.4(MTFMT):​c.*97_*99dupTTT 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 0.0023 (2 hom., cov: 0)
  • Exomes 𝑓: 0.019 (2 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.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.019 (4999/262434) while in subpopulation NFE AF= 0.0205 (3943/192368). AF 95% confidence interval is 0.02. There are 2 homozygotes in gnomad4_exome. There are 2563 alleles in male gnomad4_exome subpopulation. Median coverage is 2. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00225 AC: 135 AN: 59988 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00112

Gnomad AMI AF: 0.00579

Gnomad AMR AF: 0.00120

Gnomad ASJ AF: 0.00168

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00175

Gnomad FIN AF: 0.00200

Gnomad MID AF: 0.00943

Gnomad NFE AF: 0.00305

Gnomad OTH AF: 0.00132

GnomAD4 exome AF: 0.0190 AC: 4999 AN: 262434 Hom.: 2 Cov.: 2 AF XY: 0.0192 AC XY: 2563 AN XY: 133202

Gnomad4 AFR exome AF: 0.0113

Gnomad4 AMR exome AF: 0.0184

Gnomad4 ASJ exome AF: 0.0197

Gnomad4 EAS exome AF: 0.00516

Gnomad4 SAS exome AF: 0.0196

Gnomad4 FIN exome AF: 0.0192

Gnomad4 NFE exome AF: 0.0205

Gnomad4 OTH exome AF: 0.0173

GnomAD4 genome AF: 0.00225 AC: 135 AN: 59970 Hom.: 2 Cov.: 0 AF XY: 0.00217 AC XY: 59 AN XY: 27130

Gnomad4 AFR AF: 0.00112

Gnomad4 AMR AF: 0.00120

Gnomad4 ASJ AF: 0.00168

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00176

Gnomad4 FIN AF: 0.00200

Gnomad4 NFE AF: 0.00305

Gnomad4 OTH AF: 0.00132

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;