rs2236014

Variant names:

• chr6-152989197-A-G
• rs2236014
• NM_019041.7:c.*698T>C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_019041.7(MTRF1L):​c.*698T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0090 (2 hom., cov: 3)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTRF1L NM_019041.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85

Genes affected

MTRF1L (HGNC:21051): (mitochondrial translation release factor 1 like) The protein encoded by this gene plays a role in mitochondrial translation termination, and is thought to be a release factor that is involved in the dissociation of the complete protein from the final tRNA, the ribosome, and the cognate mRNA. This protein acts upon UAA and UAG stop codons, but has no in vitro activity against UGA, which encodes tryptophan in human mitochondrion, or, the mitochondrial non-cognate stop codons, AGA and AGG. This protein shares sequence similarity to bacterial release factors. Pseudogenes of this gene are found on chromosomes 4, 8, and 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2014]

ENSG00000227627 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTRF1L	NM_019041.7	c.*698T>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000367233.10	NP_061914.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTRF1L	ENST00000367233	c.*698T>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_019041.7	ENSP00000356202.5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 427 AN: 47554 Hom.: 2 Cov.: 3 FAILED QC

Gnomad AFR AF: 0.00871

Gnomad AMI AF: 0.0170

Gnomad AMR AF: 0.00962

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0109

Gnomad SAS AF: 0.0107

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0147

Gnomad NFE AF: 0.00803

Gnomad OTH AF: 0.00525

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00899 AC: 427 AN: 47522 Hom.: 2 Cov.: 3 AF XY: 0.00937 AC XY: 215 AN XY: 22938

Gnomad4 AFR AF: 0.00872

Gnomad4 AMR AF: 0.00963

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.0109

Gnomad4 SAS AF: 0.0106

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.00803

Gnomad4 OTH AF: 0.00524

Alfa AF: 0.157 Hom.: 240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.70

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: rs2236014; hg19: chr6-153310332;