19-57660933-C-A

Variant names:

• chr19-57660933-C-A
• rs11881170
• NM_001384833.1:c.-429+803C>A

Variant summary

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

Score: -12 - Benign

-12

BP4_StrongBA1

The NM_001384833.1(ZSCAN4):​c.-429+803C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,956 control chromosomes in the GnomAD database, including 24,512 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 0.56 (24512 hom., cov: 31)
• Consequence: ZSCAN4 NM_001384833.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 3 publications found

Genes affected

ZSCAN4 (HGNC:23709): (zinc finger and SCAN domain containing 4) The ZSCAN4 gene encodes a protein involved in telomere maintenance and with a key role in the critical feature of mouse embryonic stem (ES) cells, namely, defying cellular senescence and maintaining normal karyotype for many cell divisions in culture (Zalzman et al., 2010 [PubMed 20336070]).[supplied by OMIM, May 2010]

ENSG00000295889 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN4	NM_001384833.1	c.-429+803C>A		intron_variant	Intron 3 of 6		NP_001371762.1
ZSCAN4	XM_017026458.1	c.-429+803C>A		intron_variant	Intron 1 of 4		XP_016881947.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295889	ENST00000733546.1	n.255+901C>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85762 AN: 151838 Hom.: 24486 Cov.: 31

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.565 AC: 85836 AN: 151956 Hom.: 24512 Cov.: 31 AF XY: 0.562 AC XY: 41755 AN XY: 74246

African (AFR) AF: 0.609 AC: 25263 AN: 41454

American (AMR) AF: 0.509 AC: 7774 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3470

East Asian (EAS) AF: 0.576 AC: 2971 AN: 5162

South Asian (SAS) AF: 0.332 AC: 1597 AN: 4814

European-Finnish (FIN) AF: 0.572 AC: 6030 AN: 10538

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38143 AN: 67936

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.515 Hom.: 3691

Bravo AF: 0.570

Asia WGS AF: 0.501 AC: 1742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.23
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11881170; hg19: chr19-58172301;