rs2523722

chr6-30197496-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003449.5(TRIM26):c.535-750G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,034 control chromosomes in the GnomAD database, including 4,279 homozygotes. 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 0.22 (4279 hom., cov: 31)
• Consequence: TRIM26 NM_003449.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132

Genes affected

TRIM26 (HGNC:12962): (tripartite motif containing 26) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic bodies. Although the function of the protein is unknown, the RING domain suggests that the protein may have DNA-binding activity. The gene localizes to the major histocompatibility complex (MHC) class I region on chromosome 6. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jun 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM26	NM_003449.5	c.535-750G>A		intron_variant		ENST00000454678.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM26	ENST00000454678.7	c.535-750G>A		intron_variant		1	NM_003449.5	P1
TRIM26	ENST00000437089.5	c.535-750G>A		intron_variant		1		P1
TRIM26	ENST00000453195.5	c.535-750G>A		intron_variant		1		P1
TRIM26	ENST00000416596.5	c.535-750G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33637 AN: 151916 Hom.: 4262 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0798

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.222 AC: 33703 AN: 152034 Hom.: 4279 Cov.: 31 AF XY: 0.213 AC XY: 15853 AN XY: 74346

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.0801

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.226

Alfa AF: 0.203 Hom.: 1859

Bravo AF: 0.237

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	9.2
Dann	Benign	0.31

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: rs2523722; hg19: chr6-30165273;