rs11635570

chr15-65002565-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_139242.4(MTFMT):c.*497T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,064 control chromosomes in the GnomAD database, including 10,143 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.34 (10143 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTFMT NM_139242.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 15-65002565-A-G is Benign according to our data. Variant chr15-65002565-A-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTFMT	NM_139242.4	c.*497T>C		3_prime_UTR_variant	9/9	ENST00000220058.9
MTFMT	XM_005254158.6	c.*497T>C		3_prime_UTR_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTFMT	ENST00000220058.9	c.*497T>C		3_prime_UTR_variant	9/9	1	NM_139242.4	P1
MTFMT	ENST00000558460.5			downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51601 AN: 151944 Hom.: 10145 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.366

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.339 AC: 51602 AN: 152064 Hom.: 10143 Cov.: 31 AF XY: 0.337 AC XY: 25029 AN XY: 74332

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.364

Alfa AF: 0.419 Hom.: 13621

Bravo AF: 0.321

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.3
Dann	Benign	0.62

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: rs11635570; hg19: chr15-65294903;