ENST00000515535.1:n.161-7813A>G

Variant names:

• chr19-58052081-T-G
• rs2123443730
• NM_182572.4:c.466-409T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_182572.4(ZSCAN1):​c.466-409T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ZSCAN1 NM_182572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 0 publications found

Genes affected

ZSCAN1 (HGNC:23712): (zinc finger and SCAN domain containing 1) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000288830 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN1	NM_182572.4	c.466-409T>G		intron_variant	Intron 4 of 5	ENST00000282326.6	NP_872378.3
ZSCAN1	XM_006723149.3	c.586-409T>G		intron_variant	Intron 3 of 4		XP_006723212.1
ZSCAN1	XM_047438630.1	c.187-409T>G		intron_variant	Intron 1 of 2		XP_047294586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN1	ENST00000282326.6	c.466-409T>G		intron_variant	Intron 4 of 5	2	NM_182572.4	ENSP00000282326.1
ENSG00000288830	ENST00000812539.1	n.157+3131A>C		intron_variant	Intron 1 of 1
ENSG00000288830	ENST00000812540.1	n.128-1814A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.68
DANN	Benign	0.54
PhyloP100		-2.6

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

Other links and lift over

dbSNP: rs2123443730; hg19: chr19-58563449;