rs9261535

chr6-30159546-G-Achr6-30159546-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM10	NM_006778.4	c.430-301C>T		intron_variant		ENST00000449742.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM10	ENST00000449742.7	c.430-301C>T		intron_variant		1	NM_006778.4	P1
TRIM10	ENST00000376704.3	c.430-301C>T		intron_variant		1

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

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.0893

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.132

Alfa AF: 0.210 Hom.: 6198

Bravo AF: 0.160

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.4
Dann	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261535; hg19: chr6-30127323;