NM_001023560.4:c.539-1178A>C

Variant names:

• chr6-28275017-A-C
• rs1419183
• NM_001023560.4:c.539-1178A>C

Variant summary

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

The NM_001023560.4(ZSCAN26):​c.539-1178A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,002 control chromosomes in the GnomAD database, including 2,510 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 0.17 (2510 hom., cov: 32)
• Consequence: ZSCAN26 NM_001023560.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 28 publications found

Genes affected

ZSCAN26 (HGNC:12978): (zinc finger and SCAN domain containing 26) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000276302 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN26	NM_001023560.4	c.539-1178A>C		intron_variant	Intron 3 of 3	ENST00000421553.7	NP_001018854.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN26	ENST00000421553.7	c.539-1178A>C		intron_variant	Intron 3 of 3	1	NM_001023560.4	ENSP00000481707.1
ENSG00000276302	ENST00000621053.1	c.133+2230A>C		intron_variant	Intron 3 of 3	4		ENSP00000481142.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25407 AN: 151884 Hom.: 2505 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0809

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0513

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.167 AC: 25428 AN: 152002 Hom.: 2510 Cov.: 32 AF XY: 0.161 AC XY: 11936 AN XY: 74348

African (AFR) AF: 0.270 AC: 11183 AN: 41398

American (AMR) AF: 0.143 AC: 2186 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0809 AC: 281 AN: 3472

East Asian (EAS) AF: 0.126 AC: 652 AN: 5170

South Asian (SAS) AF: 0.0906 AC: 437 AN: 4826

European-Finnish (FIN) AF: 0.0671 AC: 710 AN: 10576

Middle Eastern (MID) AF: 0.0483 AC: 14 AN: 290

European-Non Finnish (NFE) AF: 0.140 AC: 9530 AN: 67984

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.153 Hom.: 4943

Bravo AF: 0.181

Asia WGS AF: 0.107 AC: 373 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.4
DANN	Benign	0.39
PhyloP100		0.065

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: rs1419183; hg19: chr6-28242794;