dbSNP rs1543922: ZNF175:c.199+66C>T (chr19-51581583-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007147.4(ZNF175):c.199+66C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0331 in 1,570,738 control chromosomes in the GnomAD database, including 4,967 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 0.11 ( 2209 hom., cov: 32)

Exomes 𝑓: 0.025 ( 2758 hom. )

Consequence

ZNF175
NM_007147.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550

Publications

9 publications found

Variant links:

Genes affected

ZNF175 (HGNC:12964): (zinc finger protein 175) Enables DNA-binding transcription activator activity, RNA polymerase II-specific; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Located in cytosol; intermediate filament cytoskeleton; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF175 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF175	NM_007147.4 link	c.199+66C>T		intron_variant	Intron 3 of 4	ENST00000262259.7	NP_009078.1	Q9Y473

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZNF175	ENST00000262259.7 link	c.199+66C>T	intron_variant	Intron 3 of 4	1	NM_007147.4	ENSP00000262259.2	Q9Y473
ZNF175	ENST00000436511.2 link	c.199+66C>T	intron_variant	Intron 2 of 3	2		ENSP00000440578.1	G3V1K8
ZNF175	ENST00000600460.1 link	n.150+66C>T	intron_variant	Intron 1 of 2	2
ZNF175	ENST00000596504.1 link	c.*52C>T	downstream_gene_variant		2		ENSP00000470922.1	M0R013

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16599

AN:

152044

Hom.:

2207

Cov.:

show subpopulations

Gnomad AFR

AF:

0.315

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0956

Gnomad ASJ

AF:

0.00865

Gnomad EAS

AF:

0.141

Gnomad SAS

AF:

0.0296

Gnomad FIN

AF:

0.0419

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.00866

Gnomad OTH

AF:

0.0877

GnomAD4 exome

AF:

0.0249

AC:

35379

AN:

1418576

Hom.:

2758

Cov.:

AF XY:

0.0235

AC XY:

16443

AN XY:

700462

show subpopulations

African (AFR)

AF:

0.330

AC:

10721

AN:

32442

American (AMR)

AF:

0.0924

AC:

3705

AN:

40112

Ashkenazi Jewish (ASJ)

AF:

0.00976

AC:

223

AN:

22848

East Asian (EAS)

AF:

0.148

AC:

5800

AN:

39296

South Asian (SAS)

AF:

0.0247

AC:

1947

AN:

78872

European-Finnish (FIN)

AF:

0.0375

AC:

1941

AN:

51734

Middle Eastern (MID)

AF:

0.0360

AC:

199

AN:

5534

European-Non Finnish (NFE)

AF:

0.00753

AC:

8202

AN:

1089266

Other (OTH)

AF:

0.0452

AC:

2641

AN:

58472

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1695

3390

5086

6781

8476

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

610

1220

1830

2440

3050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.109

AC:

16622

AN:

152162

Hom.:

2209

Cov.:

AF XY:

0.110

AC XY:

8155

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.314

AC:

13023

AN:

41450

American (AMR)

AF:

0.0956

AC:

1463

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00865

AC:

AN:

3470

East Asian (EAS)

AF:

0.141

AC:

732

AN:

5180

South Asian (SAS)

AF:

0.0292

AC:

141

AN:

4832

European-Finnish (FIN)

AF:

0.0419

AC:

444

AN:

10604

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00866

AC:

589

AN:

68014

Other (OTH)

AF:

0.0868

AC:

183

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

611

1222

1834

2445

3056

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

162

324

486

648

810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0436

Hom.:

2770

Bravo

AF:

0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.3

(source)

DANN

Benign

0.64

PhyloP100

0.055

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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