chr6-30152113-G-T

Variant names:

• chr6-30152113-G-T
• rs9468692
• NM_006778.4:c.*1856C>A

Variant summary

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

The NM_006778.4(TRIM10):​c.*1856C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,054 control chromosomes in the GnomAD database, including 1,316 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 0.11 (1316 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM10	NM_006778.4	c.*1856C>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000449742.7	NP_006769.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM10	ENST00000449742	c.*1856C>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_006778.4	ENSP00000397073.2
TRIM10	ENST00000376704	c.*1575C>A		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000365894.3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16425 AN: 151936 Hom.: 1314 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0711

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.00962

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.114

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: 0.108 AC: 16451 AN: 152054 Hom.: 1316 Cov.: 32 AF XY: 0.105 AC XY: 7826 AN XY: 74334

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0710

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.00984

Gnomad4 SAS AF: 0.0787

Gnomad4 FIN AF: 0.0618

Gnomad4 NFE AF: 0.0743

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0749 Hom.: 732

Bravo AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.33
DANN	Benign	0.66

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;