rs2844775

Variant names:

• chr6-30211645-G-A
• rs2844775
• NM_003449.5:c.-376+1660C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-30211645-G-A
• chr6-30211645-G-C
• chr6-30211645-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003449.5(TRIM26):​c.-376+1660C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,094 control chromosomes in the GnomAD database, including 3,450 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 0.20 (3450 hom., cov: 32)
• Consequence: TRIM26 NM_003449.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 36 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]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.245 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM26	NM_003449.5	MANE Select	c.-376+1660C>T		intron	N/A	NP_003440.1
	TRIM26	NM_001242783.2		c.-155+1660C>T		intron	N/A	NP_001229712.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM26	ENST00000454678.7	TSL:1 MANE Select	c.-376+1660C>T		intron	N/A	ENSP00000410446.2
	TRIM26	ENST00000453195.5	TSL:1	c.-155+1660C>T		intron	N/A	ENSP00000391879.1
	TRIM26	ENST00000861717.1		c.-250+1660C>T		intron	N/A	ENSP00000531776.1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29675 AN: 151976 Hom.: 3448 Cov.: 32

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.195 AC: 29689 AN: 152094 Hom.: 3450 Cov.: 32 AF XY: 0.197 AC XY: 14675 AN XY: 74348

African (AFR) AF: 0.0766 AC: 3177 AN: 41500

American (AMR) AF: 0.230 AC: 3510 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1090 AN: 5178

South Asian (SAS) AF: 0.120 AC: 581 AN: 4824

European-Finnish (FIN) AF: 0.314 AC: 3317 AN: 10552

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16839 AN: 67978

Other (OTH) AF: 0.157 AC: 332 AN: 2114

Alfa AF: 0.219 Hom.: 10547

Bravo AF: 0.183

Asia WGS AF: 0.151 AC: 524 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.70
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2844775; hg19: chr6-30179422;