rs2288421

Positions:

• chr19-53068053-T-C

Variant summary

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

The NM_001322131.2(ZNF160):​c.*24A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 1,565,046 control chromosomes in the GnomAD database, including 62,914 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 0.23 (5007 hom., cov: 32)
  • Exomes 𝑓: 0.28 (57907 hom.)
• Consequence: ZNF160 NM_001322131.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

Genes affected

ZNF160 (HGNC:12948): (zinc finger protein 160) The protein encoded by this gene is a Kruppel-related zinc finger protein which is characterized by the presence of an N-terminal repressor domain, the Kruppel-associated box (KRAB). The KRAB domain is a potent repressor of transcription; thus this protein may function in transcription regulation. Multiple transcript variants have been found for this gene. [provided by RefSeq, Apr 2016]

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 = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF160	NM_001322131.2	c.*24A>G		3_prime_UTR_variant	6/6	ENST00000683776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF160	ENST00000683776.1	c.*24A>G		3_prime_UTR_variant	6/6		NM_001322131.2	P1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35159 AN: 151994 Hom.: 4999 Cov.: 32

Gnomad AFR AF: 0.0772

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.235

GnomAD3 exomes AF: 0.268 AC: 57486 AN: 214510 Hom.: 8554 AF XY: 0.265 AC XY: 30123 AN XY: 113850

Gnomad AFR exome AF: 0.0671

Gnomad AMR exome AF: 0.358

Gnomad ASJ exome AF: 0.266

Gnomad EAS exome AF: 0.300

Gnomad SAS exome AF: 0.126

Gnomad FIN exome AF: 0.296

Gnomad NFE exome AF: 0.292

Gnomad OTH exome AF: 0.281

GnomAD4 exome AF: 0.281 AC: 397208 AN: 1412934 Hom.: 57907 Cov.: 32 AF XY: 0.276 AC XY: 192709 AN XY: 697362

Gnomad4 AFR exome AF: 0.0653

Gnomad4 AMR exome AF: 0.353

Gnomad4 ASJ exome AF: 0.268

Gnomad4 EAS exome AF: 0.328

Gnomad4 SAS exome AF: 0.128

Gnomad4 FIN exome AF: 0.295

Gnomad4 NFE exome AF: 0.294

Gnomad4 OTH exome AF: 0.269

GnomAD4 genome AF: 0.231 AC: 35176 AN: 152112 Hom.: 5007 Cov.: 32 AF XY: 0.234 AC XY: 17394 AN XY: 74344

Gnomad4 AFR AF: 0.0770

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.234

Alfa AF: 0.274 Hom.: 8480

Bravo AF: 0.231

Asia WGS AF: 0.194 AC: 676 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	1.5
DANN	Benign	0.60

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: rs2288421; hg19: chr19-53571306; COSMIC: COSV105268163; COSMIC: COSV105268163;