Genetic Variant NM_001350984.2:c.806-21705T>G (chr7-99647390-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001350984.2(ZSCAN25):c.806-21705T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0653 in 691,652 control chromosomes in the GnomAD database, including 5,717 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 0.15 ( 3928 hom., cov: 32)

Exomes 𝑓: 0.040 ( 1789 hom. )

Consequence

ZSCAN25
NM_001350984.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.98

Publications

11 publications found

Variant links:

Genes affected

ZSCAN25 (HGNC:21961): (zinc finger and SCAN domain containing 25) This gene encodes a protein that bears some similarity to zinc finger proteins, which are involved in DNA binding and protein-protein interactions. Multiple alternatively spliced transcript variants have been identified, but the full-length nature for most of them has not been determined. [provided by RefSeq, Jul 2008]

ZSCAN25 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
ZSCAN25	NM_001350984.2 link	c.806-21705T>G	intron_variant	Intron 7 of 7	NP_001337913.1
ZSCAN25	NM_001350985.2 link	c.806-21705T>G	intron_variant	Intron 5 of 5	NP_001337914.1
ZSCAN25	XM_011515909.3 link	c.806-21705T>G	intron_variant	Intron 7 of 7	XP_011514211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23388

AN:

151932

Hom.:

3912

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.0386

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.259

Gnomad FIN

AF:

0.0145

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0243

Gnomad OTH

AF:

0.133

GnomAD4 exome

AF:

0.0402

AC:

21713

AN:

539600

Hom.:

1789

AF XY:

0.0397

AC XY:

10056

AN XY:

253276

show subpopulations

African (AFR)

AF:

0.449

AC:

4860

AN:

10828

American (AMR)

AF:

0.119

AC:

AN:

632

Ashkenazi Jewish (ASJ)

AF:

0.0304

AC:

100

AN:

3294

East Asian (EAS)

AF:

0.273

AC:

653

AN:

2392

South Asian (SAS)

AF:

0.238

AC:

2565

AN:

10790

European-Finnish (FIN)

AF:

0.00556

AC:

AN:

180

Middle Eastern (MID)

AF:

0.0648

AC:

AN:

1064

European-Non Finnish (NFE)

AF:

0.0243

AC:

11994

AN:

492800

Other (OTH)

AF:

0.0792

AC:

1396

AN:

17620

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

866

1731

2597

3462

4328

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.154

AC:

23448

AN:

152052

Hom.:

3928

Cov.:

AF XY:

0.157

AC XY:

11635

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.399

AC:

16534

AN:

41424

American (AMR)

AF:

0.134

AC:

2045

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0386

AC:

134

AN:

3470

East Asian (EAS)

AF:

0.266

AC:

1381

AN:

5182

South Asian (SAS)

AF:

0.258

AC:

1242

AN:

4818

European-Finnish (FIN)

AF:

0.0145

AC:

153

AN:

10560

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0243

AC:

1649

AN:

67994

Other (OTH)

AF:

0.133

AC:

280

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

802

1604

2407

3209

4011

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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:

0.0720

Hom.:

4141

Bravo

AF:

0.169

Asia WGS

AF:

0.272

AC:

945

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.097

(source)

DANN

Benign

0.47

PhyloP100

-2.0

Splicing

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