16-3436236-C-T

Variant names:

• chr16-3436236-C-T
• rs37824
• NM_152457.3:c.*188G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152457.3(ZNF597):​c.*188G>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 0.237 in 621,426 control chromosomes in the GnomAD database, including 17,957 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 0.25 (4823 hom., cov: 32)
  • Exomes 𝑓: 0.23 (13134 hom.)
• Consequence: ZNF597 NM_152457.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 12 publications found

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]

ENSG00000285329 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF597	NM_152457.3	c.*188G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000301744.7	NP_689670.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF597	ENST00000301744.7	c.*188G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_152457.3	ENSP00000301744.4
ENSG00000285329	ENST00000575785.2	n.212-12235C>T		intron_variant	Intron 2 of 4	4		ENSP00000477472.1

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37660 AN: 151932 Hom.: 4801 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.234 AC: 109609 AN: 469376 Hom.: 13134 Cov.: 5 AF XY: 0.235 AC XY: 57632 AN XY: 245446

African (AFR) AF: 0.321 AC: 4127 AN: 12860

American (AMR) AF: 0.191 AC: 3116 AN: 16336

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 3272 AN: 13708

East Asian (EAS) AF: 0.155 AC: 4762 AN: 30634

South Asian (SAS) AF: 0.282 AC: 11832 AN: 41952

European-Finnish (FIN) AF: 0.198 AC: 5694 AN: 28782

Middle Eastern (MID) AF: 0.216 AC: 426 AN: 1976

European-Non Finnish (NFE) AF: 0.237 AC: 70173 AN: 296662

Other (OTH) AF: 0.235 AC: 6207 AN: 26466

GnomAD4 genome AF: 0.248 AC: 37735 AN: 152050 Hom.: 4823 Cov.: 32 AF XY: 0.243 AC XY: 18051 AN XY: 74324

African (AFR) AF: 0.317 AC: 13135 AN: 41442

American (AMR) AF: 0.203 AC: 3107 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3468

East Asian (EAS) AF: 0.150 AC: 776 AN: 5174

South Asian (SAS) AF: 0.261 AC: 1257 AN: 4822

European-Finnish (FIN) AF: 0.179 AC: 1888 AN: 10566

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15858 AN: 67990

Other (OTH) AF: 0.228 AC: 481 AN: 2114

Alfa AF: 0.212 Hom.: 1798

Bravo AF: 0.254

Asia WGS AF: 0.242 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.062
DANN	Benign	0.50
PhyloP100		-1.7
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: rs37824; hg19: chr16-3486236;