16-3436285-C-A

Position:

• chr16-3436285-C-A

Variant summary

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

The NM_152457.3(ZNF597):​c.*139G>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 0.831 in 825,182 control chromosomes in the GnomAD database, including 285,916 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 0.80 (48775 hom., cov: 33)
  • Exomes 𝑓: 0.84 (237141 hom.)
• Consequence: ZNF597 NM_152457.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

ZNF597 (HGNC:26573): (zinc finger protein 597) This gene encodes a protein with multiple zinc finger domains. Loss of the related gene in rodents results in defects in neural development and embryonic lethality in mutant homozygotes. This gene is adjacent to a differentially methylated region (DMR) and is imprinted and maternally expressed. [provided by RefSeq, Nov 2015]

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 (AMR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF597	NM_152457.3	c.*139G>T		3_prime_UTR_variant	4/4	ENST00000301744.7	NP_689670.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF597	ENST00000301744.7	c.*139G>T		3_prime_UTR_variant	4/4	1	NM_152457.3	ENSP00000301744	P1

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121287 AN: 152066 Hom.: 48744 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.785

GnomAD4 exome AF: 0.838 AC: 564237 AN: 672998 Hom.: 237141 Cov.: 9 AF XY: 0.839 AC XY: 287452 AN XY: 342768

Gnomad4 AFR exome AF: 0.681

Gnomad4 AMR exome AF: 0.882

Gnomad4 ASJ exome AF: 0.781

Gnomad4 EAS exome AF: 0.845

Gnomad4 SAS exome AF: 0.840

Gnomad4 FIN exome AF: 0.831

Gnomad4 NFE exome AF: 0.846

Gnomad4 OTH exome AF: 0.820

GnomAD4 genome AF: 0.798 AC: 121373 AN: 152184 Hom.: 48775 Cov.: 33 AF XY: 0.798 AC XY: 59375 AN XY: 74394

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.785

Alfa AF: 0.828 Hom.: 54005

Bravo AF: 0.797

Asia WGS AF: 0.838 AC: 2914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.51

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: rs12737; hg19: chr16-3486285; COSMIC: COSV57086217;