rs34704748

chr19-19680067-CAT-Cchr19-19680067-CAT-CATAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_033204.4(ZNF101):c.1080_1081del(p.His360GlnfsTer7) variant causes a frameshift change. The variant allele was found at a frequency of 0.0285 in 1,614,076 control chromosomes in the GnomAD database, including 804 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.021 (44 hom., cov: 32)
  • Exomes 𝑓: 0.029 (760 hom.)
• Consequence: ZNF101 NM_033204.4 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.74

Genes affected

ZNF101 (HGNC:12881): (zinc finger protein 101) Zinc finger proteins (ZNFs), such as ZNF101, bind nucleic acids and perform many key functions, the most important of which is regulating transcription (summary by Bellefroid et al., 1993 [PubMed 8467795]). See ZNF91 (MIM 603971) for general information on ZNFs.[supplied by OMIM, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0207 (3150/152218) while in subpopulation NFE AF= 0.0328 (2231/68006). AF 95% confidence interval is 0.0317. There are 44 homozygotes in gnomad4. There are 1416 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 44 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF101	NM_033204.4	c.1080_1081del	p.His360GlnfsTer7	frameshift_variant	4/4	ENST00000592502.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF101	ENST00000592502.2	c.1080_1081del	p.His360GlnfsTer7	frameshift_variant	4/4	1	NM_033204.4	P1

Frequencies

GnomAD3 genomes AF: 0.0207 AC: 3150 AN: 152100 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.00589

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00621

Gnomad FIN AF: 0.0156

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0328

Gnomad OTH AF: 0.0249

GnomAD3 exomes AF: 0.0210 AC: 5275 AN: 251352 Hom.: 101 AF XY: 0.0213 AC XY: 2899 AN XY: 135882

Gnomad AFR exome AF: 0.00523

Gnomad AMR exome AF: 0.0107

Gnomad ASJ exome AF: 0.0284

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00777

Gnomad FIN exome AF: 0.0164

Gnomad NFE exome AF: 0.0332

Gnomad OTH exome AF: 0.0279

GnomAD4 exome AF: 0.0294 AC: 42910 AN: 1461858 Hom.: 760 AF XY: 0.0289 AC XY: 20997 AN XY: 727226

Gnomad4 AFR exome AF: 0.00493

Gnomad4 AMR exome AF: 0.0118

Gnomad4 ASJ exome AF: 0.0286

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.00804

Gnomad4 FIN exome AF: 0.0172

Gnomad4 NFE exome AF: 0.0342

Gnomad4 OTH exome AF: 0.0261

GnomAD4 genome AF: 0.0207 AC: 3150 AN: 152218 Hom.: 44 Cov.: 32 AF XY: 0.0190 AC XY: 1416 AN XY: 74430

Gnomad4 AFR AF: 0.00590

Gnomad4 AMR AF: 0.0170

Gnomad4 ASJ AF: 0.0282

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00642

Gnomad4 FIN AF: 0.0156

Gnomad4 NFE AF: 0.0328

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.00770 Hom.: 15

Bravo AF: 0.0211

Asia WGS AF: 0.00606 AC: 21 AN: 3478

EpiCase AF: 0.0354

EpiControl AF: 0.0317

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs34704748; hg19: chr19-19790876;