chr1-39883663-CT-C

Variant names:

• chr1-39883663-CT-C
• rs58870544
• NR_183424.1:n.272+255delT

Variant summary

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

The NR_183424.1(MYCL-AS1):​n.272+255delT 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 NR_183424.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796

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]

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 31 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIT1	NM_017646.6	c.-173delA		upstream_gene_variant		ENST00000316891.10	NP_060116.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIT1	ENST00000316891.10	c.-173delA		upstream_gene_variant		1	NM_017646.6	ENSP00000321810.5
TRIT1	ENST00000372818.5	c.-173delA		upstream_gene_variant		1		ENSP00000361905.1
TRIT1	ENST00000462797.5	n.-173delA		upstream_gene_variant		5		ENSP00000473773.1
TRIT1	ENST00000486825.6	n.-191delA		upstream_gene_variant		5		ENSP00000474151.1
TRIT1	ENST00000489945.5	n.-173delA		upstream_gene_variant		5		ENSP00000473745.1
TRIT1	ENST00000492612.6	n.-185delA		upstream_gene_variant		5		ENSP00000473708.1

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

Gnomad4 AFR AF: 0.0311

Gnomad4 AMR AF: 0.00455

Gnomad4 ASJ AF: 0.000294

Gnomad4 EAS AF: 0.000595

Gnomad4 SAS AF: 0.000658

Gnomad4 FIN AF: 0.00579

Gnomad4 NFE AF: 0.00127

Gnomad4 OTH AF: 0.0106

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: rs58870544; hg19: chr1-40349335;