rs3132671

Positions:

• chr6-30210510-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.-376+2795G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,988 control chromosomes in the GnomAD database, including 13,725 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 0.42 (13725 hom., cov: 31)
• Consequence: TRIM26 NM_003449.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

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]

TRIM26 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM26	NM_003449.5	c.-376+2795G>A		intron_variant		ENST00000454678.7	NP_003440.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM26	ENST00000454678.7	c.-376+2795G>A		intron_variant		1	NM_003449.5	ENSP00000410446.2

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64117 AN: 151870 Hom.: 13697 Cov.: 31

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.422 AC: 64200 AN: 151988 Hom.: 13725 Cov.: 31 AF XY: 0.419 AC XY: 31130 AN XY: 74284

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.389

Alfa AF: 0.435 Hom.: 21801

Bravo AF: 0.420

Asia WGS AF: 0.375 AC: 1304 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.084
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132671; hg19: chr6-30178287;