7-99521178-C-T

Variant names:

• chr7-99521178-C-T
• rs11761528
• NM_145102.4:c.772+874C>T

Variant summary

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

The NM_145102.4(ZKSCAN5):​c.772+874C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,008 control chromosomes in the GnomAD database, including 1,357 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 0.12 (1357 hom., cov: 32)
• Consequence: ZKSCAN5 NM_145102.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 36 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZKSCAN5	NM_145102.4	c.772+874C>T		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.772+874C>T		intron_variant	Intron 5 of 6	1	NM_145102.4	ENSP00000322872.5
ZKSCAN5	ENST00000394170.6	c.772+874C>T		intron_variant	Intron 5 of 6	1		ENSP00000377725.2
ZKSCAN5	ENST00000451158.5	c.772+874C>T		intron_variant	Intron 5 of 6	1		ENSP00000392104.1
ZKSCAN5	ENST00000454175.1	n.636+1269C>T		intron_variant	Intron 3 of 4	1		ENSP00000405716.1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17976 AN: 151890 Hom.: 1348 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0551

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0659

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0829

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.118 AC: 18013 AN: 152008 Hom.: 1357 Cov.: 32 AF XY: 0.120 AC XY: 8926 AN XY: 74290

African (AFR) AF: 0.207 AC: 8564 AN: 41434

American (AMR) AF: 0.0843 AC: 1284 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5184

South Asian (SAS) AF: 0.0664 AC: 320 AN: 4818

European-Finnish (FIN) AF: 0.152 AC: 1607 AN: 10564

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5633 AN: 67988

Other (OTH) AF: 0.121 AC: 255 AN: 2110

Alfa AF: 0.0890 Hom.: 2377

Bravo AF: 0.116

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.64
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: rs11761528; hg19: chr7-99118801;