6-28423688-A-G

Variant names:

• chr6-28423688-A-G
• rs2859365
• XR_007059223.1:n.6893T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007059223.1(ZSCAN23):​n.6893T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,068 control chromosomes in the GnomAD database, including 19,117 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 0.48 (19117 hom., cov: 32)
• Consequence: ZSCAN23 XR_007059223.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 32 publications found

Genes affected

ZSCAN23 (HGNC:21193): (zinc finger and SCAN domain containing 23) 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]

ENSG00000310015 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846572.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310015	ENST00000846572.1		n.54-12A>G		intron	N/A
	ENSG00000310015	ENST00000846573.1		n.103-12A>G		intron	N/A
	ENSG00000310015	ENST00000846574.1		n.412-12A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72950 AN: 151950 Hom.: 19087 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.480 AC: 73038 AN: 152068 Hom.: 19117 Cov.: 32 AF XY: 0.476 AC XY: 35393 AN XY: 74344

African (AFR) AF: 0.696 AC: 28875 AN: 41476

American (AMR) AF: 0.477 AC: 7287 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1598 AN: 3470

East Asian (EAS) AF: 0.519 AC: 2688 AN: 5182

South Asian (SAS) AF: 0.463 AC: 2228 AN: 4814

European-Finnish (FIN) AF: 0.327 AC: 3452 AN: 10572

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25370 AN: 67974

Other (OTH) AF: 0.487 AC: 1027 AN: 2110

Alfa AF: 0.427 Hom.: 32700

Bravo AF: 0.504

Asia WGS AF: 0.464 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.72
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs2859365; hg19: chr6-28391465;