rs2288421

Variant names:

• chr19-53068053-T-C
• rs2288421
• NM_001322131.2:c.*24A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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]

ENSG00000306331 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322131.2. 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
	ZNF160	NM_001322131.2	MANE Select	c.*24A>G		3_prime_UTR	Exon 6 of 6	NP_001309060.1	Q9HCG1-1
	ZNF160	NM_001102603.2		c.*24A>G		3_prime_UTR	Exon 7 of 7	NP_001096073.1	Q9HCG1-1
	ZNF160	NM_001322128.2		c.*24A>G		3_prime_UTR	Exon 7 of 7	NP_001309057.1	Q9HCG1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF160	ENST00000683776.1	MANE Select	c.*24A>G		3_prime_UTR	Exon 6 of 6	ENSP00000507845.1	Q9HCG1-1
	ZNF160	ENST00000418871.5	TSL:1	c.*24A>G		3_prime_UTR	Exon 6 of 6	ENSP00000409597.1	Q9HCG1-1
	ZNF160	ENST00000599056.5	TSL:1	c.*24A>G		3_prime_UTR	Exon 7 of 7	ENSP00000470961.1	Q9HCG1-1

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

GnomAD2 exomes AF: 0.268 AC: 57486 AN: 214510 AF XY: 0.265

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 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

African (AFR) AF: 0.0653 AC: 2115 AN: 32368

American (AMR) AF: 0.353 AC: 13974 AN: 39602

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 6050 AN: 22616

East Asian (EAS) AF: 0.328 AC: 12902 AN: 39286

South Asian (SAS) AF: 0.128 AC: 9909 AN: 77224

European-Finnish (FIN) AF: 0.295 AC: 15256 AN: 51638

Middle Eastern (MID) AF: 0.248 AC: 1141 AN: 4598

European-Non Finnish (NFE) AF: 0.294 AC: 320180 AN: 1087390

Other (OTH) AF: 0.269 AC: 15681 AN: 58212

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

African (AFR) AF: 0.0770 AC: 3197 AN: 41528

American (AMR) AF: 0.354 AC: 5406 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3472

East Asian (EAS) AF: 0.292 AC: 1510 AN: 5174

South Asian (SAS) AF: 0.133 AC: 642 AN: 4826

European-Finnish (FIN) AF: 0.307 AC: 3243 AN: 10560

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19327 AN: 67972

Other (OTH) AF: 0.234 AC: 495 AN: 2112

Alfa AF: 0.271 Hom.: 10492

Bravo AF: 0.231

Asia WGS AF: 0.194 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.60
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2288421;

hg19: chr19-53571306;

COSMIC: COSV105268163;

COSMIC: COSV105268163;