NM_001385745.1:c.*913T>C

Variant names:

• chr12-6666801-A-G
• rs6786
• NM_001385745.1:c.*913T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001385745.1(ZNF384):​c.*913T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 170,308 control chromosomes in the GnomAD database, including 36,289 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 0.64 (33442 hom., cov: 30)
  • Exomes 𝑓: 0.48 (2847 hom.)
• Consequence: ZNF384 NM_001385745.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23
• Publications: 7 publications found

Genes affected

ZNF384 (HGNC:11955): (zinc finger protein 384) This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. [provided by RefSeq, Apr 2011]

ENSG00000219410 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF384	NM_001385745.1	c.*913T>C		3_prime_UTR_variant	Exon 12 of 12	ENST00000683879.1	NP_001372674.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF384	ENST00000683879.1	c.*913T>C		3_prime_UTR_variant	Exon 12 of 12		NM_001385745.1	ENSP00000507462.1

Frequencies

GnomAD3 genomes AF: 0.641 AC: 95919 AN: 149638 Hom.: 33397 Cov.: 30

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.445

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.573

GnomAD4 exome AF: 0.483 AC: 9962 AN: 20604 Hom.: 2847 Cov.: 0 AF XY: 0.480 AC XY: 4570 AN XY: 9522

African (AFR) AF: 0.895 AC: 614 AN: 686

American (AMR) AF: 0.489 AC: 214 AN: 438

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 539 AN: 1326

East Asian (EAS) AF: 0.0747 AC: 294 AN: 3934

South Asian (SAS) AF: 0.549 AC: 90 AN: 164

European-Finnish (FIN) AF: 0.581 AC: 243 AN: 418

Middle Eastern (MID) AF: 0.462 AC: 60 AN: 130

European-Non Finnish (NFE) AF: 0.587 AC: 6964 AN: 11870

Other (OTH) AF: 0.576 AC: 944 AN: 1638

GnomAD4 genome AF: 0.641 AC: 96005 AN: 149704 Hom.: 33442 Cov.: 30 AF XY: 0.628 AC XY: 45905 AN XY: 73074

African (AFR) AF: 0.902 AC: 37046 AN: 41062

American (AMR) AF: 0.516 AC: 7738 AN: 14986

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1390 AN: 3466

East Asian (EAS) AF: 0.113 AC: 583 AN: 5162

South Asian (SAS) AF: 0.532 AC: 2553 AN: 4800

European-Finnish (FIN) AF: 0.509 AC: 4805 AN: 9434

Middle Eastern (MID) AF: 0.451 AC: 128 AN: 284

European-Non Finnish (NFE) AF: 0.592 AC: 39954 AN: 67540

Other (OTH) AF: 0.575 AC: 1184 AN: 2060

Alfa AF: 0.568 Hom.: 8312

Bravo AF: 0.648

Asia WGS AF: 0.396 AC: 1363 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		2.2
Mutation Taster		=100/0	polymorphism (auto)

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: rs6786; hg19: chr12-6775967;