chr1-39883663-CT-C

Variant names:

• chr1-39883663-CT-C
• rs58870544
• ENST00000418255.2:n.325+480delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000418255.2(MYCL-AS1):​n.325+480delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 146,012 control chromosomes in the GnomAD database, including 31 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.010 (31 hom., cov: 30)
• Consequence: MYCL-AS1 ENST00000418255.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796
• Publications: 0 publications found

Genes affected

MYCL-AS1 (HGNC:40386): (MYCL antisense RNA 1)

TRIT1 (HGNC:20286): (tRNA isopentenyltransferase 1) This gene encodes a protein that that is targeted to the mitochondrion and modifies transfer RNAs (tRNAs) by adding a dimethylallyl group onto the adenine at position 37. This modification is important for maintaining the correct reading frame during protein translation. This gene is considered a tumor suppressor and its expression can decrease cell growth. Alternative splicing results in multiple transcripts variants, most of which are likely non-functional. [provided by RefSeq, Aug 2015]

TRIT1 Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• combined oxidative phosphorylation deficiency 35

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0101 (1479/146012) while in subpopulation AFR AF = 0.0311 (1248/40156). AF 95% confidence interval is 0.0296. There are 31 homozygotes in GnomAd4. There are 739 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 31 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418255.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYCL-AS1	NR_183424.1		n.272+255delT		intron	N/A
	MYCL-AS1	NR_183425.1		n.35+492delT		intron	N/A
	TRIT1	NM_017646.6	MANE Select	c.-173delA		upstream_gene	N/A	NP_060116.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYCL-AS1	ENST00000418255.2	TSL:2	n.325+480delT		intron	N/A
	MYCL-AS1	ENST00000837551.1		n.303+243delT		intron	N/A
	TRIT1	ENST00000316891.10	TSL:1 MANE Select	c.-173delA		upstream_gene	N/A	ENSP00000321810.5	Q9H3H1-1

Frequencies

GnomAD3 genomes AF: 0.0100 AC: 1467 AN: 145978 Hom.: 31 Cov.: 30

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00455

Gnomad ASJ AF: 0.000294

Gnomad EAS AF: 0.000593

Gnomad SAS AF: 0.000437

Gnomad FIN AF: 0.00579

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00127

Gnomad OTH AF: 0.00961

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0101 AC: 1479 AN: 146012 Hom.: 31 Cov.: 30 AF XY: 0.0104 AC XY: 739 AN XY: 71010

African (AFR) AF: 0.0311 AC: 1248 AN: 40156

American (AMR) AF: 0.00455 AC: 67 AN: 14732

Ashkenazi Jewish (ASJ) AF: 0.000294 AC: 1 AN: 3400

East Asian (EAS) AF: 0.000595 AC: 3 AN: 5044

South Asian (SAS) AF: 0.000658 AC: 3 AN: 4558

European-Finnish (FIN) AF: 0.00579 AC: 52 AN: 8984

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 276

European-Non Finnish (NFE) AF: 0.00127 AC: 84 AN: 65980

Other (OTH) AF: 0.0106 AC: 21 AN: 1990

Alfa AF: 0.00 Hom.: 15

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs58870544; hg19: chr1-40349335;