NM_033204.4:c.1080_1081delTA

Variant names:

• chr19-19680067-CAT-C
• rs34704748
• NM_033204.4:c.1080_1081delTA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_033204.4(ZNF101):​c.1080_1081delTA​(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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 44 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033204.4. 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
	ZNF101	NM_033204.4	MANE Select	c.1080_1081delTA	p.His360GlnfsTer7	frameshift	Exon 4 of 4	NP_149981.2
	ZNF101	NM_001300949.2		c.720_721delTA	p.His240GlnfsTer7	frameshift	Exon 4 of 4	NP_001287878.1	Q8IZC7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF101	ENST00000592502.2	TSL:1 MANE Select	c.1080_1081delTA	p.His360GlnfsTer7	frameshift	Exon 4 of 4	ENSP00000468049.1	Q8IZC7-1
	ZNF101	ENST00000415784.6	TSL:1	c.720_721delTA	p.His240GlnfsTer7	frameshift	Exon 5 of 5	ENSP00000400952.2	Q8IZC7-2
	ZNF101	ENST00000318110.9	TSL:5	n.1080_1081delTA		non_coding_transcript_exon	Exon 4 of 5	ENSP00000319716.5	Q8IZC7-1

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

GnomAD2 exomes AF: 0.0210 AC: 5275 AN: 251352 AF XY: 0.0213

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 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

African (AFR) AF: 0.00493 AC: 165 AN: 33480

American (AMR) AF: 0.0118 AC: 527 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0286 AC: 747 AN: 26136

East Asian (EAS) AF: 0.0000504 AC: 2 AN: 39700

South Asian (SAS) AF: 0.00804 AC: 693 AN: 86230

European-Finnish (FIN) AF: 0.0172 AC: 919 AN: 53420

Middle Eastern (MID) AF: 0.0369 AC: 213 AN: 5768

European-Non Finnish (NFE) AF: 0.0342 AC: 38065 AN: 1112006

Other (OTH) AF: 0.0261 AC: 1579 AN: 60394

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

African (AFR) AF: 0.00590 AC: 245 AN: 41518

American (AMR) AF: 0.0170 AC: 260 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 98 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00642 AC: 31 AN: 4826

European-Finnish (FIN) AF: 0.0156 AC: 165 AN: 10608

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0328 AC: 2231 AN: 68006

Other (OTH) AF: 0.0246 AC: 52 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.7
Mutation Taster		=183/17	polymorphism (auto)

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

Other links and lift over

dbSNP: rs34704748; hg19: chr19-19790876; COSMIC: COSV58909054; COSMIC: COSV58909054;