dbSNP rs17720293: ZKSCAN4:c.778+49G>A (chr6-28246920-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_019110.5(ZKSCAN4):c.778+49G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,571,792 control chromosomes in the GnomAD database, including 9,878 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 0.071 ( 498 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9380 hom. )

Consequence

ZKSCAN4
NM_019110.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.19

Publications

34 publications found

Variant links:

Genes affected

ZKSCAN4 (HGNC:13854): (zinc finger with KRAB and SCAN domains 4) Enables identical protein binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZKSCAN4 links:

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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=-0.72).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019110.5. 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
	ZKSCAN4	NM_019110.5	MANE Select	c.778+49G>A		intron	N/A	NP_061983.2
	ZKSCAN4	NM_001304506.2		c.313+49G>A		intron	N/A	NP_001291435.1	B7Z7H3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZKSCAN4	ENST00000377294.3	TSL:1 MANE Select	c.778+49G>A	intron	N/A	ENSP00000366509.2	Q969J2
ZKSCAN4	ENST00000959508.1		c.778+49G>A	intron	N/A	ENSP00000629567.1
ZKSCAN4	ENST00000927146.1		c.760+49G>A	intron	N/A	ENSP00000597205.1

Frequencies

GnomAD3 genomes

AF:

0.0710

AC:

10795

AN:

152110

Hom.:

497

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0428

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.0470

Gnomad ASJ

AF:

0.0225

Gnomad EAS

AF:

0.00750

Gnomad SAS

AF:

0.00995

Gnomad FIN

AF:

0.0568

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.0608

GnomAD2 exomes

AF:

0.0637

AC:

14067

AN:

220976

AF XY:

0.0638

show subpopulations

Gnomad AFR exome

AF:

0.0437

Gnomad AMR exome

AF:

0.0298

Gnomad ASJ exome

AF:

0.0235

Gnomad EAS exome

AF:

0.00667

Gnomad FIN exome

AF:

0.0611

Gnomad NFE exome

AF:

0.102

Gnomad OTH exome

AF:

0.0622

GnomAD4 exome

AF:

0.105

AC:

149380

AN:

1419564

Hom.:

9380

Cov.:

AF XY:

0.102

AC XY:

71741

AN XY:

704214

show subpopulations

African (AFR)

AF:

0.0415

AC:

1329

AN:

32062

American (AMR)

AF:

0.0312

AC:

1223

AN:

39198

Ashkenazi Jewish (ASJ)

AF:

0.0236

AC:

558

AN:

23606

East Asian (EAS)

AF:

0.0243

AC:

943

AN:

38734

South Asian (SAS)

AF:

0.0119

AC:

942

AN:

79054

European-Finnish (FIN)

AF:

0.0609

AC:

3170

AN:

52024

Middle Eastern (MID)

AF:

0.0202

AC:

112

AN:

5538

European-Non Finnish (NFE)

AF:

0.125

AC:

136091

AN:

1090822

Other (OTH)

AF:

0.0856

AC:

5012

AN:

58526

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

5541

11082

16624

22165

27706

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5056

10112

15168

20224

25280

<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:

0.0709

AC:

10788

AN:

152228

Hom.:

498

Cov.:

AF XY:

0.0648

AC XY:

4827

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.0426

AC:

1771

AN:

41544

American (AMR)

AF:

0.0469

AC:

716

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0225

AC:

AN:

3470

East Asian (EAS)

AF:

0.00752

AC:

AN:

5188

South Asian (SAS)

AF:

0.0102

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0568

AC:

603

AN:

10608

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7269

AN:

68000

Other (OTH)

AF:

0.0597

AC:

126

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

507

1014

1522

2029

2536

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:

0.0872

Hom.:

1205

Bravo

AF:

0.0696

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

1.7

(source)

DANN

Benign

0.81

PhyloP100

-2.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over