rs10493052

chr1-33480084-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001377376.1(ZSCAN20):c.417+379C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,200 control chromosomes in the GnomAD database, including 1,451 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 0.13 (1451 hom., cov: 32)
• Consequence: ZSCAN20 NM_001377376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533

Genes affected

ZSCAN20 (HGNC:13093): (zinc finger and SCAN domain containing 20) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSCAN20	NM_001377376.1	c.417+379C>A		intron_variant		ENST00000684572.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN20	ENST00000684572.1	c.417+379C>A		intron_variant			NM_001377376.1	P1
ZSCAN20	ENST00000373413.2	c.417+379C>A		intron_variant		1
ZSCAN20	ENST00000361328.7	c.417+379C>A		intron_variant		2		P1
ZSCAN20	ENST00000480917.1	n.559+379C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20301 AN: 152082 Hom.: 1450 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.0936

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.134 AC: 20322 AN: 152200 Hom.: 1451 Cov.: 32 AF XY: 0.130 AC XY: 9652 AN XY: 74388

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.0933

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.0871

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.137

Alfa AF: 0.143 Hom.: 2272

Bravo AF: 0.132

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.9
Dann	Benign	0.39

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

LitVar

Other links and lift over

dbSNP: rs10493052; hg19: chr1-33945685;