chr6-28270281-T-C

Variant names:

• chr6-28270281-T-C
• rs67998226
• NM_001023560.4:c.-66-1573T>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.-66-1573T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 152,282 control chromosomes in the GnomAD database, including 374 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 0.062 (374 hom., cov: 32)
• Consequence: ZSCAN26 NM_001023560.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 15 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0864 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001023560.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN26	NM_001023560.4	MANE Select	c.-66-1573T>C		intron	N/A	NP_001018854.2	A0A024RCN4
	ZSCAN26	NM_001111039.3		c.-66-1573T>C		intron	N/A	NP_001104509.1	Q16670-1
	ZSCAN26	NM_001287421.2		c.-66-1573T>C		intron	N/A	NP_001274350.1	A0A087X2F1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN26	ENST00000421553.7	TSL:1 MANE Select	c.-66-1573T>C		intron	N/A	ENSP00000481707.1	A0A024RCN4
	ZSCAN26	ENST00000316606.10	TSL:1	c.-66-1573T>C		intron	N/A	ENSP00000484931.1	A0A087X2F1
	ENSG00000276302	ENST00000621053.1	TSL:4	c.-66-1573T>C		intron	N/A	ENSP00000481142.1	A0A087WXM4

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9433 AN: 152164 Hom.: 374 Cov.: 32

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0274

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0397

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0883

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0619 AC: 9429 AN: 152282 Hom.: 374 Cov.: 32 AF XY: 0.0561 AC XY: 4174 AN XY: 74450

African (AFR) AF: 0.0557 AC: 2313 AN: 41558

American (AMR) AF: 0.0273 AC: 418 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4826

European-Finnish (FIN) AF: 0.0397 AC: 421 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0882 AC: 6001 AN: 68008

Other (OTH) AF: 0.0397 AC: 84 AN: 2116

Alfa AF: 0.0749 Hom.: 131

Bravo AF: 0.0616

Asia WGS AF: 0.00577 AC: 22 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	0.43
DANN	Benign	0.61
PhyloP100		-0.71

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: rs67998226; hg19: chr6-28238059;