dbSNP rs34704748: ZNF101:p.His360GlnfsTer7 (chr19-19680067-CAT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.74

Publications

6 publications found

Variant links:

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]

ZNF101 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF101	NM_033204.4 link	c.1080_1081delTA	p.His360GlnfsTer7	frameshift_variant	Exon 4 of 4	ENST00000592502.2	NP_149981.2	Q8IZC7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF101	ENST00000592502.2 link	c.1080_1081delTA	p.His360GlnfsTer7	frameshift_variant	Exon 4 of 4	1	NM_033204.4	ENSP00000468049.1		Q8IZC7-1

Frequencies

GnomAD3 genomes

AF:

0.0207

AC:

3150

AN:

152100

Hom.:

Cov.:

show subpopulations

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

show subpopulations

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

show subpopulations

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:

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

2475

4951

7426

9902

12377

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0207

AC:

3150

AN:

152218

Hom.:

Cov.:

AF XY:

0.0190

AC XY:

1416

AN XY:

74430

show subpopulations

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:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5192

South Asian (SAS)

AF:

0.00642

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0156

AC:

165

AN:

10608

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0328

AC:

2231

AN:

68006

Other (OTH)

AF:

0.0246

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

165

330

494

659

824

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00770

Hom.:

Bravo

AF:

0.0211

Asia WGS

AF:

0.00606

AC:

AN:

3478

EpiCase

AF:

0.0354

EpiControl

AF:

0.0317

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

6.7

Mutation Taster

=183/17

polymorphism (auto)

(source)

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

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rs34704748

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over