rs967005

Positions:

• chr6-28242910-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.*2206G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,142 control chromosomes in the GnomAD database, including 3,604 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 0.20 (3604 hom., cov: 33)
• Consequence: ZKSCAN4 NM_019110.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZKSCAN4	NM_019110.5	c.*2206G>A		3_prime_UTR_variant	5/5	ENST00000377294.3	NP_061983.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZKSCAN4	ENST00000377294.3	c.*2206G>A		3_prime_UTR_variant	5/5	1	NM_019110.5	ENSP00000366509	P1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31031 AN: 152024 Hom.: 3592 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.204 AC: 31073 AN: 152142 Hom.: 3604 Cov.: 33 AF XY: 0.197 AC XY: 14684 AN XY: 74420

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0954

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.182

Alfa AF: 0.174 Hom.: 4831

Bravo AF: 0.217

Asia WGS AF: 0.165 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	14
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs967005; hg19: chr6-28210688;