rs9468692

chr6-30152113-G-Achr6-30152113-G-Cchr6-30152113-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_006778.4(TRIM10):c.*1856C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00495 in 152,080 control chromosomes in the GnomAD database, including 10 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 0.0050 (10 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TRIM10 NM_006778.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

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=-0.92).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00495 (753/152080) while in subpopulation EAS AF= 0.0421 (218/5184). AF 95% confidence interval is 0.0375. There are 10 homozygotes in gnomad4. There are 418 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM10	NM_006778.4	c.*1856C>T		3_prime_UTR_variant	7/7	ENST00000449742.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM10	ENST00000449742.7	c.*1856C>T		3_prime_UTR_variant	7/7	1	NM_006778.4	P1
TRIM10	ENST00000376704.3	c.*1575C>T		3_prime_UTR_variant	8/8	1

Frequencies

GnomAD3 genomes AF: 0.00497 AC: 755 AN: 151962 Hom.: 10 Cov.: 32

Gnomad AFR AF: 0.000726

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00780

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0420

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.00313

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00375

Gnomad OTH AF: 0.00526

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.00495 AC: 753 AN: 152080 Hom.: 10 Cov.: 32 AF XY: 0.00562 AC XY: 418 AN XY: 74344

Gnomad4 AFR AF: 0.000724

Gnomad4 AMR AF: 0.00778

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.0421

Gnomad4 SAS AF: 0.0145

Gnomad4 FIN AF: 0.00313

Gnomad4 NFE AF: 0.00375

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.0000527 Hom.: 732

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.76
Dann	Benign	0.62

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: rs9468692; hg19: chr6-30119890;