Genetic Variant ZSCAN16-AS1:n.188+19908C>A (chr6-28040470-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000660873.1(ZSCAN16-AS1):n.188+19908C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 152,092 control chromosomes in the GnomAD database, including 294 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 0.052 ( 294 hom., cov: 32)

Consequence

ZSCAN16-AS1
ENST00000660873.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

Publications

0 publications found

Variant links:

Genes affected

ZSCAN16-AS1 (HGNC:48982): (ZSCAN16 antisense RNA 1)

ZSCAN16-AS1 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=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ZSCAN16-AS1	ENST00000660873.1 link	n.188+19908C>A	intron_variant	Intron 2 of 3
ZSCAN16-AS1	ENST00000716089.1 link	n.223+19908C>A	intron_variant	Intron 2 of 2
ZSCAN16-AS1	ENST00000716090.1 link	n.310+19908C>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0514

AC:

7811

AN:

151974

Hom.:

291

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0192

Gnomad AMI

AF:

0.0879

Gnomad AMR

AF:

0.0641

Gnomad ASJ

AF:

0.0406

Gnomad EAS

AF:

0.0986

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.0981

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0506

Gnomad OTH

AF:

0.0430

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

GnomAD4 genome

AF:

0.0516

AC:

7848

AN:

152092

Hom.:

294

Cov.:

AF XY:

0.0549

AC XY:

4079

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.0196

AC:

813

AN:

41512

American (AMR)

AF:

0.0646

AC:

987

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0406

AC:

141

AN:

3470

East Asian (EAS)

AF:

0.0992

AC:

512

AN:

5162

South Asian (SAS)

AF:

0.153

AC:

739

AN:

4822

European-Finnish (FIN)

AF:

0.0981

AC:

1036

AN:

10556

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0506

AC:

3438

AN:

67980

Other (OTH)

AF:

0.0440

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

366

732

1099

1465

1831

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<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:

0.0471

Hom.:

Bravo

AF:

0.0453

Asia WGS

AF:

0.171

AC:

593

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.18

(source)

DANN

Benign

0.51

PhyloP100

-1.5

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over