rs12912

chr7-101097504-G-Achr7-101097504-G-C

Variant summary

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

The NM_030961.3(TRIM56):c.*7924G>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 0.577 in 151,994 control chromosomes in the GnomAD database, including 25,801 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 0.58 (25798 hom., cov: 32)
  • Exomes 𝑓: 0.67 (3 hom.)
• Consequence: TRIM56 NM_030961.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

Genes affected

TRIM56 (HGNC:19028): (tripartite motif containing 56) Enables RNA binding activity. Predicted to be involved in several processes, including defense response to other organism; positive regulation of macromolecule metabolic process; and protein K63-linked ubiquitination. Predicted to be located in cytoplasm. Predicted to be active in chromatin and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM56	NM_030961.3	c.*7924G>A		3_prime_UTR_variant	3/3	ENST00000306085.11
TRIM56	XM_011516589.4	c.*7924G>A		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM56	ENST00000306085.11	c.*7924G>A		3_prime_UTR_variant	3/3	1	NM_030961.3	P1

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87627 AN: 151864 Hom.: 25780 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.565

GnomAD4 exome AF: 0.667 AC: 8 AN: 12 Hom.: 3 Cov.: 0 AF XY: 0.750 AC XY: 6 AN XY: 8

Gnomad4 NFE exome AF: 0.700

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.577 AC: 87675 AN: 151982 Hom.: 25798 Cov.: 32 AF XY: 0.572 AC XY: 42439 AN XY: 74256

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.564

Alfa AF: 0.630 Hom.: 44666

Bravo AF: 0.566

Asia WGS AF: 0.536 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	2.3
Dann	Benign	0.78

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: rs12912; hg19: chr7-100740785;