rs9261547

Variant names:

• chr6-30187151-G-A
• rs9261547
• NM_003449.5:c.938-593C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003449.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM26	NM_003449.5	MANE Select	c.938-593C>T		intron	N/A	NP_003440.1
	TRIM26	NM_001242783.2		c.938-593C>T		intron	N/A	NP_001229712.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM26	ENST00000454678.7	TSL:1 MANE Select	c.938-593C>T		intron	N/A	ENSP00000410446.2
	TRIM26	ENST00000437089.5	TSL:1	c.938-593C>T		intron	N/A	ENSP00000395491.1
	TRIM26	ENST00000453195.5	TSL:1	c.938-593C>T		intron	N/A	ENSP00000391879.1

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

African (AFR) AF: 0.978 AC: 2436 AN: 2492

American (AMR) AF: 0.969 AC: 6595 AN: 6808

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 2655 AN: 2802

East Asian (EAS) AF: 0.978 AC: 4137 AN: 4232

South Asian (SAS) AF: 0.947 AC: 20574 AN: 21734

European-Finnish (FIN) AF: 0.893 AC: 9992 AN: 11192

Middle Eastern (MID) AF: 0.919 AC: 432 AN: 470

European-Non Finnish (NFE) AF: 0.892 AC: 63903 AN: 71662

Other (OTH) AF: 0.896 AC: 5638 AN: 6294

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

African (AFR) AF: 0.968 AC: 40230 AN: 41550

American (AMR) AF: 0.933 AC: 14281 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3266 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5053 AN: 5188

South Asian (SAS) AF: 0.946 AC: 4568 AN: 4828

European-Finnish (FIN) AF: 0.882 AC: 9341 AN: 10592

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59677 AN: 68028

Other (OTH) AF: 0.918 AC: 1943 AN: 2116

Alfa AF: 0.894 Hom.: 154157

Bravo AF: 0.924

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.50
PhyloP100		2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9261547; hg19: chr6-30154928;