rs2859365

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN23	XR_007059223.1	n.6893T>C		non_coding_transcript_exon_variant	Exon 6 of 6
ZSCAN23	XR_007059224.1	n.7005T>C		non_coding_transcript_exon_variant	Exon 7 of 7
ZSCAN23	XR_007059225.1	n.7203T>C		non_coding_transcript_exon_variant	Exon 6 of 6
ZSCAN23	XR_007059226.1	n.3702T>C		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310015	ENST00000846572.1	n.54-12A>G		intron_variant	Intron 1 of 2
ENSG00000310015	ENST00000846573.1	n.103-12A>G		intron_variant	Intron 1 of 2
ENSG00000310015	ENST00000846574.1	n.412-12A>G		intron_variant	Intron 2 of 2
ENSG00000310015	ENST00000846575.1	n.95-12A>G		intron_variant	Intron 1 of 1

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 v4.3

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;