rs11976018

chr7-99524814-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ZKSCAN5	NM_145102.4	c.773-999G>A		intron_variant		ENST00000326775.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZKSCAN5	ENST00000326775.10	c.773-999G>A		intron_variant		1	NM_145102.4	P1
ZKSCAN5	ENST00000394170.6	c.773-999G>A		intron_variant		1		P1
ZKSCAN5	ENST00000451158.5	c.773-999G>A		intron_variant		1		P1
ZKSCAN5	ENST00000454175.1	c.637-999G>A		intron_variant, NMD_transcript_variant		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

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.343

Alfa AF: 0.190 Hom.: 5332

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11976018; hg19: chr7-99122437;