rs2299030

Variant names:

• chr6-28230977-T-C
• rs2299030
• NM_006299.5:c.569-1585T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006299.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN9	NM_006299.5	MANE Select	c.569-1585T>C		intron	N/A	NP_006290.1
	ZSCAN9	NM_001199479.2		c.721+489T>C		intron	N/A	NP_001186408.1
	ZSCAN9	NM_001199480.2		c.569-1585T>C		intron	N/A	NP_001186409.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN9	ENST00000252207.10	TSL:1 MANE Select	c.569-1585T>C		intron	N/A	ENSP00000252207.5
	ZSCAN9	ENST00000425468.6	TSL:1	c.721+489T>C		intron	N/A	ENSP00000404074.2
	ZSCAN9	ENST00000526391.5	TSL:1	c.569-1585T>C		intron	N/A	ENSP00000476254.1

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

African (AFR) AF: 0.0106 AC: 442 AN: 41524

American (AMR) AF: 0.0404 AC: 618 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3470

East Asian (EAS) AF: 0.0692 AC: 358 AN: 5170

South Asian (SAS) AF: 0.0501 AC: 242 AN: 4828

European-Finnish (FIN) AF: 0.0273 AC: 289 AN: 10590

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0379 AC: 2579 AN: 68008

Other (OTH) AF: 0.0293 AC: 62 AN: 2116

Alfa AF: 0.0372 Hom.: 179

Bravo AF: 0.0307

Asia WGS AF: 0.0420 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.84
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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: rs2299030; hg19: chr6-28198755;