rs17720293

chr6-28246920-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019110.5(ZKSCAN4):c.778+49G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,571,792 control chromosomes in the GnomAD database, including 9,878 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 0.071 (498 hom., cov: 32)
  • Exomes 𝑓: 0.11 (9380 hom.)
• Consequence: ZKSCAN4 NM_019110.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

Genes affected

ZKSCAN4 (HGNC:13854): (zinc finger with KRAB and SCAN domains 4) Enables identical protein binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in 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=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZKSCAN4	NM_019110.5	c.778+49G>A		intron_variant		ENST00000377294.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZKSCAN4	ENST00000377294.3	c.778+49G>A		intron_variant		1	NM_019110.5	P1

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10795 AN: 152110 Hom.: 497 Cov.: 32

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.00750

Gnomad SAS AF: 0.00995

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0608

GnomAD3 exomes AF: 0.0637 AC: 14067 AN: 220976 Hom.: 672 AF XY: 0.0638 AC XY: 7609 AN XY: 119316

Gnomad AFR exome AF: 0.0437

Gnomad AMR exome AF: 0.0298

Gnomad ASJ exome AF: 0.0235

Gnomad EAS exome AF: 0.00667

Gnomad SAS exome AF: 0.0115

Gnomad FIN exome AF: 0.0611

Gnomad NFE exome AF: 0.102

Gnomad OTH exome AF: 0.0622

GnomAD4 exome AF: 0.105 AC: 149380 AN: 1419564 Hom.: 9380 Cov.: 29 AF XY: 0.102 AC XY: 71741 AN XY: 704214

Gnomad4 AFR exome AF: 0.0415

Gnomad4 AMR exome AF: 0.0312

Gnomad4 ASJ exome AF: 0.0236

Gnomad4 EAS exome AF: 0.0243

Gnomad4 SAS exome AF: 0.0119

Gnomad4 FIN exome AF: 0.0609

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.0856

GnomAD4 genome AF: 0.0709 AC: 10788 AN: 152228 Hom.: 498 Cov.: 32 AF XY: 0.0648 AC XY: 4827 AN XY: 74444

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.00752

Gnomad4 SAS AF: 0.0102

Gnomad4 FIN AF: 0.0568

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0893 Hom.: 716

Bravo AF: 0.0696

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	1.7
Dann	Benign	0.81

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: rs17720293; hg19: chr6-28214698;