1-39883663-C-CT

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NR_183424.1(MYCL-AS1):​n.272+255dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0793 in 146,096 control chromosomes in the GnomAD database, including 577 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.079 (577 hom., cov: 30)
• Consequence: MYCL-AS1 NR_183424.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 -10 ACMG points.

• BP6: Variant 1-39883663-C-CT is Benign according to our data. Variant chr1-39883663-C-CT is described in ClinVar as [Benign]. Clinvar id is 1276471.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIT1	NM_017646.6	c.-173dupA		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.-173_-172insA		upstream_gene_variant		1	NM_017646.6	ENSP00000321810.5
TRIT1	ENST00000372818.5	c.-173_-172insA		upstream_gene_variant		1		ENSP00000361905.1
TRIT1	ENST00000462797.5	n.-173_-172insA		upstream_gene_variant		5		ENSP00000473773.1
TRIT1	ENST00000486825.6	n.-191_-190insA		upstream_gene_variant		5		ENSP00000474151.1
TRIT1	ENST00000489945.5	n.-173_-172insA		upstream_gene_variant		5		ENSP00000473745.1
TRIT1	ENST00000492612.6	n.-185_-184insA		upstream_gene_variant		5		ENSP00000473708.1

Frequencies

GnomAD3 genomes AF: 0.0793 AC: 11581 AN: 146060 Hom.: 577 Cov.: 30

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00119

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0793 AC: 11579 AN: 146096 Hom.: 577 Cov.: 30 AF XY: 0.0777 AC XY: 5518 AN XY: 71038

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.0957

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.00119

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0770

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 06, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;