chr1-26054237-C-CT

Position:

• chr1-26054237-C-CT

Variant summary

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

The NM_032588.4(TRIM63):​c.980-274_980-273insA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.80 (49768 hom., cov: 0)
• Consequence: TRIM63 NM_032588.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.113

Genes affected

TRIM63 (HGNC:16007): (tripartite motif containing 63) This gene encodes a member of the RING zinc finger protein family found in striated muscle and iris. The product of this gene is an E3 ubiquitin ligase that localizes to the Z-line and M-line lattices of myofibrils. This protein plays an important role in the atrophy of skeletal and cardiac muscle and is required for the degradation of myosin heavy chain proteins, myosin light chain, myosin binding protein, and for muscle-type creatine kinase. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-26054237-C-CT is Benign according to our data. Variant chr1-26054237-C-CT is described in ClinVar as [Benign]. Clinvar id is 1269179.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM63	NM_032588.4	c.980-274_980-273insA		intron_variant		ENST00000374272.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM63	ENST00000374272.4	c.980-274_980-273insA		intron_variant		1	NM_032588.4	P1

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120980 AN: 152034 Hom.: 49741 Cov.: 0

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.796 AC: 121050 AN: 152152 Hom.: 49768 Cov.: 0 AF XY: 0.799 AC XY: 59446 AN XY: 74402

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.792

Alfa AF: 0.833 Hom.: 6537

Bravo AF: 0.782

Asia WGS AF: 0.841 AC: 2924 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 04, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11424290; hg19: chr1-26380728;