6-28275017-A-C

Position:

• chr6-28275017-A-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZSCAN26	NM_001023560.4	c.539-1178A>C		intron_variant		ENST00000421553.7	NP_001018854.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN26	ENST00000421553.7	c.539-1178A>C		intron_variant		1	NM_001023560.4	ENSP00000481707

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

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0809

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0906

Gnomad4 FIN AF: 0.0671

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.144

Alfa AF: 0.137 Hom.: 2156

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

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: rs1419183; hg19: chr6-28242794;