rs9261547

Positions:

• chr6-30187151-G-A
• chr6-30187151-G-C

Variant summary

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

The NM_003449.5(TRIM26):​c.938-593C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 279,968 control chromosomes in the GnomAD database, including 117,230 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 0.92 (64067 hom., cov: 32)
  • Exomes 𝑓: 0.91 (53163 hom.)
• Consequence: TRIM26 NM_003449.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99

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]

PAIP1P1 (HGNC:18240): (PAIP1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM26	NM_003449.5	c.938-593C>T		intron_variant		ENST00000454678.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM26	ENST00000454678.7	c.938-593C>T		intron_variant		1	NM_003449.5	P1
PAIP1P1	ENST00000446875.1	n.850C>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139373 AN: 152164 Hom.: 64001 Cov.: 32

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.917

GnomAD4 exome AF: 0.911 AC: 116362 AN: 127686 Hom.: 53163 Cov.: 0 AF XY: 0.917 AC XY: 64264 AN XY: 70050

Gnomad4 AFR exome AF: 0.978

Gnomad4 AMR exome AF: 0.969

Gnomad4 ASJ exome AF: 0.948

Gnomad4 EAS exome AF: 0.978

Gnomad4 SAS exome AF: 0.947

Gnomad4 FIN exome AF: 0.893

Gnomad4 NFE exome AF: 0.892

Gnomad4 OTH exome AF: 0.896

GnomAD4 genome AF: 0.916 AC: 139498 AN: 152282 Hom.: 64067 Cov.: 32 AF XY: 0.917 AC XY: 68254 AN XY: 74458

Gnomad4 AFR AF: 0.968

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.946

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.918

Alfa AF: 0.890 Hom.: 47792

Bravo AF: 0.924

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.50

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: rs9261547; hg19: chr6-30154928;