chr7-101097504-G-A

Variant names:

• chr7-101097504-G-A
• rs12912
• NM_030961.3:c.*7924G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030961.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM56	NM_030961.3	MANE Select	c.*7924G>A		3_prime_UTR	Exon 3 of 3	NP_112223.1	Q9BRZ2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM56	ENST00000306085.11	TSL:1 MANE Select	c.*7924G>A		3_prime_UTR	Exon 3 of 3	ENSP00000305161.6	Q9BRZ2-1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.700 AC: 7 AN: 10

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.495 AC: 20531 AN: 41454

American (AMR) AF: 0.469 AC: 7151 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2039 AN: 3464

East Asian (EAS) AF: 0.558 AC: 2886 AN: 5174

South Asian (SAS) AF: 0.587 AC: 2824 AN: 4814

European-Finnish (FIN) AF: 0.577 AC: 6088 AN: 10548

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.649 AC: 44091 AN: 67974

Other (OTH) AF: 0.564 AC: 1191 AN: 2110

Alfa AF: 0.618 Hom.: 73292

Bravo AF: 0.566

Asia WGS AF: 0.536 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.3
DANN	Benign	0.78
PhyloP100		-0.092

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

Other links and lift over

dbSNP: rs12912; hg19: chr7-100740785;