rs2299030

Positions:

• chr6-28230977-T-C

Variant summary

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

The NM_006299.5(ZSCAN9):​c.569-1585T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0317 in 152,206 control chromosomes in the GnomAD database, including 89 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 0.032 (89 hom., cov: 32)
• Consequence: ZSCAN9 NM_006299.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

ZSCAN9 (HGNC:12984): (zinc finger and SCAN domain containing 9) 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. [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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSCAN9	NM_006299.5	c.569-1585T>C		intron_variant		ENST00000252207.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN9	ENST00000252207.10	c.569-1585T>C		intron_variant		1	NM_006299.5	P2

Frequencies

GnomAD3 genomes AF: 0.0317 AC: 4824 AN: 152090 Hom.: 89 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.0693

Gnomad SAS AF: 0.0495

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0291

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

GnomAD4 genome AF: 0.0317 AC: 4827 AN: 152206 Hom.: 89 Cov.: 32 AF XY: 0.0310 AC XY: 2306 AN XY: 74418

Gnomad4 AFR AF: 0.0106

Gnomad4 AMR AF: 0.0404

Gnomad4 ASJ AF: 0.0478

Gnomad4 EAS AF: 0.0692

Gnomad4 SAS AF: 0.0501

Gnomad4 FIN AF: 0.0273

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0331 Hom.: 14

Bravo AF: 0.0307

Asia WGS AF: 0.0420 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.84

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: rs2299030; hg19: chr6-28198755;