dbSNP rs149990: ZSCAN16-AS1:n.189-13279C>T (chr6-28030480-G-A) – 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.189-13279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,140 control chromosomes in the GnomAD database, including 1,150 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 0.12 ( 1150 hom., cov: 32)

Consequence

ZSCAN16-AS1
ENST00000660873.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.379

Publications

23 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 (AMR) allele frequency at 95% confidence interval = 0.132 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.189-13279C>T	intron_variant	Intron 2 of 3
ZSCAN16-AS1	ENST00000716089.1 link	n.224-21472C>T	intron_variant	Intron 2 of 2
ZSCAN16-AS1	ENST00000716090.1 link	n.311-21472C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18056

AN:

152022

Hom.:

1149

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.0769

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.0929

Gnomad FIN

AF:

0.0496

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.103

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

GnomAD4 genome

AF:

0.119

AC:

18077

AN:

152140

Hom.:

1150

Cov.:

AF XY:

0.115

AC XY:

8547

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.135

AC:

5610

AN:

41506

American (AMR)

AF:

0.136

AC:

2084

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0769

AC:

267

AN:

3470

East Asian (EAS)

AF:

0.120

AC:

622

AN:

5174

South Asian (SAS)

AF:

0.0934

AC:

450

AN:

4820

European-Finnish (FIN)

AF:

0.0496

AC:

525

AN:

10592

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8175

AN:

67992

Other (OTH)

AF:

0.102

AC:

216

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

819

1638

2457

3276

4095

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.123

Hom.:

3665

Bravo

AF:

0.125

Asia WGS

AF:

0.102

AC:

354

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.9

(source)

DANN

Benign

0.35

PhyloP100

0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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