dbSNP rs1216119: ZNF98:c.48+5296G>T (chr19-22527043-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000593802.1(ZNF98):c.48+5296G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,078 control chromosomes in the GnomAD database, including 7,270 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 0.30 ( 7268 hom., cov: 32)

Exomes 𝑓: 0.35 ( 2 hom. )

Consequence

ZNF98
ENST00000593802.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.124

Publications

7 publications found

Variant links:

Genes affected

ZNF98 (HGNC:13174): (zinc finger protein 98) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF98 links:

ENSG00000260599 (HGNC:):

ENSG00000260599 links:

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new If you want to explore the variant's impact on the transcript ENST00000593802.1, 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 (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593802.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LOC101929124	NR_110427.1	n.907G>T	non_coding_transcript_exon	Exon 1 of 5
LOC105376917	NR_160727.1	n.147+5296G>T	intron	N/A
LOC105376917	NR_160728.1	n.147+5296G>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF98	ENST00000593802.1	TSL:3	c.48+5296G>T	intron	N/A	ENSP00000472301.1	M0R243
ENSG00000260599	ENST00000562262.1	TSL:2	n.907G>T	non_coding_transcript_exon	Exon 1 of 5
ZNF98	ENST00000599879.1	TSL:3	n.147+5296G>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.297

AC:

45054

AN:

151920

Hom.:

7261

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.350

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.577

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.272

Gnomad OTH

AF:

0.308

GnomAD4 exome

AF:

0.350

AC:

AN:

Hom.:

Cov.:

AF XY:

0.429

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.375

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.321

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.297

AC:

45100

AN:

152038

Hom.:

7268

Cov.:

AF XY:

0.305

AC XY:

22630

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.251

AC:

10416

AN:

41492

American (AMR)

AF:

0.350

AC:

5339

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.258

AC:

895

AN:

3470

East Asian (EAS)

AF:

0.577

AC:

2950

AN:

5112

South Asian (SAS)

AF:

0.524

AC:

2527

AN:

4822

European-Finnish (FIN)

AF:

0.343

AC:

3620

AN:

10562

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.272

AC:

18511

AN:

67984

Other (OTH)

AF:

0.307

AC:

650

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1623

3246

4868

6491

8114

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

476

952

1428

1904

2380

<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:

0.298

Hom.:

6376

Bravo

AF:

0.297

Asia WGS

AF:

0.551

AC:

1911

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

6.5

(source)

DANN

Benign

0.33

PhyloP100

0.12

Splicing

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over