6-30159546-G-A

Variant names:

• chr6-30159546-G-A
• rs9261535
• NM_006778.4:c.430-301C>T

Variant summary

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

The NM_006778.4(TRIM10):​c.430-301C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,062 control chromosomes in the GnomAD database, including 2,902 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 0.17 (2902 hom., cov: 31)
• Consequence: TRIM10 NM_006778.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 31 publications found

Genes affected

TRIM10 (HGNC:10072): (tripartite motif containing 10) 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. This protein localizes to cytoplasmic bodies. Studies in mice suggest that this protein plays a role in terminal differentiation of erythroid cells. Alternate splicing of this gene generates two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006778.4. 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
	TRIM10	NM_006778.4	MANE Select	c.430-301C>T		intron	N/A	NP_006769.2
	TRIM10	NM_052828.3		c.430-301C>T		intron	N/A	NP_439893.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM10	ENST00000449742.7	TSL:1 MANE Select	c.430-301C>T		intron	N/A	ENSP00000397073.2
	TRIM10	ENST00000376704.3	TSL:1	c.430-301C>T		intron	N/A	ENSP00000365894.3

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26245 AN: 151942 Hom.: 2900 Cov.: 31

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.173 AC: 26256 AN: 152062 Hom.: 2902 Cov.: 31 AF XY: 0.174 AC XY: 12926 AN XY: 74312

African (AFR) AF: 0.0448 AC: 1859 AN: 41492

American (AMR) AF: 0.190 AC: 2906 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3468

East Asian (EAS) AF: 0.228 AC: 1180 AN: 5168

South Asian (SAS) AF: 0.0893 AC: 430 AN: 4814

European-Finnish (FIN) AF: 0.296 AC: 3119 AN: 10546

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15781 AN: 67982

Other (OTH) AF: 0.132 AC: 279 AN: 2112

Alfa AF: 0.205 Hom.: 14141

Bravo AF: 0.160

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9261535; hg19: chr6-30127323;