6-30161172-G-T

Position:

• chr6-30161172-G-T

Variant summary

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

The NM_006778.4(TRIM10):​c.-314C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0615 in 152,244 control chromosomes in the GnomAD database, including 468 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 0.061 (468 hom., cov: 32)
• Consequence: TRIM10 NM_006778.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM10	NM_006778.4	c.-314C>A		5_prime_UTR_variant	1/7	ENST00000449742.7	NP_006769.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM10	ENST00000449742.7	c.-314C>A		5_prime_UTR_variant	1/7	1	NM_006778.4	ENSP00000397073.2

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9362 AN: 152126 Hom.: 468 Cov.: 32

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0615 AC: 9358 AN: 152244 Hom.: 468 Cov.: 32 AF XY: 0.0563 AC XY: 4188 AN XY: 74442

Gnomad4 AFR AF: 0.0179

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.0673

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0914 Hom.: 1069

Bravo AF: 0.0570

Asia WGS AF: 0.00404 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2157678; hg19: chr6-30128949;