dbSNP rs10411195: ZNF93:c.227-7815T>C (chr19-19925367-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_031218.4(ZNF93):c.227-7815T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 152,248 control chromosomes in the GnomAD database, including 977 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 0.078 ( 977 hom., cov: 31)

Consequence

ZNF93
NM_031218.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.34

Publications

11 publications found

Variant links:

Genes affected

ZNF93 (HGNC:13169): (zinc finger protein 93) Enables DNA-binding transcription factor activity. Involved in negative regulation of transcription, DNA-templated and negative regulation of transposon integration. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF93 links:

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new If you want to explore the variant's impact on the transcript NM_031218.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031218.4. 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
	ZNF93	NM_031218.4	MANE Select	c.227-7815T>C		intron	N/A	NP_112495.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF93	ENST00000343769.6	TSL:1 MANE Select	c.227-7815T>C	intron	N/A	ENSP00000342002.4	P35789-1
ZNF93	ENST00000592160.5	TSL:1	c.227-6641T>C	intron	N/A	ENSP00000467377.1	K7EPG7
ZNF93	ENST00000588146.1	TSL:4	c.35-7815T>C	intron	N/A	ENSP00000467553.1	K7EPV7

Frequencies

GnomAD3 genomes

AF:

0.0779

AC:

11849

AN:

152130

Hom.:

974

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0334

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.0576

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0132

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0217

Gnomad OTH

AF:

0.0589

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0780

AC:

11873

AN:

152248

Hom.:

977

Cov.:

AF XY:

0.0778

AC XY:

5793

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.209

AC:

8693

AN:

41516

American (AMR)

AF:

0.0334

AC:

511

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0121

AC:

AN:

3472

East Asian (EAS)

AF:

0.0576

AC:

298

AN:

5178

South Asian (SAS)

AF:

0.122

AC:

586

AN:

4820

European-Finnish (FIN)

AF:

0.0132

AC:

140

AN:

10618

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0217

AC:

1475

AN:

68024

Other (OTH)

AF:

0.0582

AC:

123

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

481

961

1442

1922

2403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<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:

0.0402

Hom.:

1042

Bravo

AF:

0.0822

Asia WGS

AF:

0.0890

AC:

313

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

3.4

(source)

DANN

Benign

0.57

PhyloP100

1.3

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

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over