rs13214023

Variant names:

• chr6-28364364-G-A
• rs13214023
• NM_024493.4:c.757+549G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-28364364-G-A
• chr6-28364364-G-T

Variant summary

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

The NM_024493.4(ZKSCAN3):​c.757+549G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0505 in 152,240 control chromosomes in the GnomAD database, including 316 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 0.051 (316 hom., cov: 32)
• Consequence: ZKSCAN3 NM_024493.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 22 publications found

Genes affected

ZKSCAN3 (HGNC:13853): (zinc finger with KRAB and SCAN domains 3) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in several processes, including negative regulation of autophagy; negative regulation of cellular senescence; and regulation of transcription, DNA-templated. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000294493 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZKSCAN3	NM_024493.4	c.757+549G>A		intron_variant	Intron 5 of 5	ENST00000252211.7	NP_077819.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZKSCAN3	ENST00000252211.7	c.757+549G>A		intron_variant	Intron 5 of 5	1	NM_024493.4	ENSP00000252211.2
ZKSCAN3	ENST00000377255.3	c.757+549G>A		intron_variant	Intron 6 of 6	1		ENSP00000366465.1
ZKSCAN3	ENST00000341464.9	c.313+549G>A		intron_variant	Intron 4 of 4	2		ENSP00000341883.5
ENSG00000294493	ENST00000723931.1	n.188-1028C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0506 AC: 7696 AN: 152122 Hom.: 316 Cov.: 32

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0393

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0877

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0505 AC: 7691 AN: 152240 Hom.: 316 Cov.: 32 AF XY: 0.0453 AC XY: 3372 AN XY: 74432

African (AFR) AF: 0.0175 AC: 729 AN: 41554

American (AMR) AF: 0.0212 AC: 325 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4818

European-Finnish (FIN) AF: 0.0393 AC: 417 AN: 10604

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0877 AC: 5961 AN: 68000

Other (OTH) AF: 0.0331 AC: 70 AN: 2114

Alfa AF: 0.0731 Hom.: 370

Bravo AF: 0.0482

Asia WGS AF: 0.00375 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.72
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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: rs13214023; hg19: chr6-28332141;