rs11976018

Variant names:

• chr7-99524814-G-A
• rs11976018
• NM_145102.4:c.773-999G>A

Variant summary

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

The NM_145102.4(ZKSCAN5):​c.773-999G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,010 control chromosomes in the GnomAD database, including 16,671 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 0.37 (16671 hom., cov: 31)
• Consequence: ZKSCAN5 NM_145102.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 9 publications found

Genes affected

ZKSCAN5 (HGNC:12867): (zinc finger with KRAB and SCAN domains 5) This gene encodes a zinc finger protein of the Kruppel family. The protein contains a SCAN box and a KRAB A domain and may be involved in transcriptional regulation. A similar protein in mouse is differentially expressed in spermatogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZKSCAN5	NM_145102.4	c.773-999G>A		intron_variant	Intron 5 of 6	ENST00000326775.10	NP_659570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZKSCAN5	ENST00000326775.10	c.773-999G>A		intron_variant	Intron 5 of 6	1	NM_145102.4	ENSP00000322872.5
ZKSCAN5	ENST00000394170.6	c.773-999G>A		intron_variant	Intron 5 of 6	1		ENSP00000377725.2
ZKSCAN5	ENST00000451158.5	c.773-999G>A		intron_variant	Intron 5 of 6	1		ENSP00000392104.1
ZKSCAN5	ENST00000454175.1	n.637-999G>A		intron_variant	Intron 3 of 4	1		ENSP00000405716.1

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55997 AN: 151890 Hom.: 16611 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.369 AC: 56119 AN: 152010 Hom.: 16671 Cov.: 31 AF XY: 0.371 AC XY: 27584 AN XY: 74304

African (AFR) AF: 0.822 AC: 34064 AN: 41442

American (AMR) AF: 0.295 AC: 4499 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1732 AN: 5158

South Asian (SAS) AF: 0.371 AC: 1787 AN: 4814

European-Finnish (FIN) AF: 0.216 AC: 2291 AN: 10586

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10297 AN: 67980

Other (OTH) AF: 0.343 AC: 723 AN: 2108

Alfa AF: 0.211 Hom.: 15983

Bravo AF: 0.393

Asia WGS AF: 0.413 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	0.32
DANN	Benign	0.46
PhyloP100		-0.39
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs11976018; hg19: chr7-99122437;