Variant 7-99533211-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_145102.4(ZKSCAN5):c.*962G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0306 in 659,584 control chromosomes in the GnomAD database, including 467 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 0.028 ( 115 hom., cov: 32)

Exomes 𝑓: 0.031 ( 352 hom. )

Consequence

ZKSCAN5
NM_145102.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.869

Variant links:

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]

ZKSCAN5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0278 (4239/152272) while in subpopulation NFE AF= 0.0355 (2413/68020). AF 95% confidence interval is 0.0343. There are 115 homozygotes in gnomad4. There are 2210 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 115 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZKSCAN5	NM_145102.4 linkuse as main transcript	c.*962G>T		3_prime_UTR_variant	7/7	ENST00000326775.10

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
ZKSCAN5	ENST00000326775.10 linkuse as main transcript	c.*962G>T	3_prime_UTR_variant	7/7	1	NM_145102.4	P1
ZKSCAN5	ENST00000394170.6 linkuse as main transcript	c.*962G>T	3_prime_UTR_variant	7/7	1		P1
ZKSCAN5	ENST00000454175.1 linkuse as main transcript	c.*2677G>T	3_prime_UTR_variant, NMD_transcript_variant	5/5	1

Frequencies

GnomAD3 genomes

AF:

0.0279

AC:

4240

AN:

152154

Hom.:

114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00673

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0241

Gnomad ASJ

AF:

0.0242

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0139

Gnomad FIN

AF:

0.0901

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0355

Gnomad OTH

AF:

0.0272

GnomAD3 exomes

AF:

0.0255

AC:

3318

AN:

130048

Hom.:

AF XY:

0.0252

AC XY:

1789

AN XY:

70972

show subpopulations

Gnomad AFR exome

AF:

0.00690

Gnomad AMR exome

AF:

0.0176

Gnomad ASJ exome

AF:

0.0234

Gnomad EAS exome

AF:

0.0000960

Gnomad SAS exome

AF:

0.0138

Gnomad FIN exome

AF:

0.0883

Gnomad NFE exome

AF:

0.0356

Gnomad OTH exome

AF:

0.0286

GnomAD4 exome

AF:

0.0314

AC:

15926

AN:

507312

Hom.:

352

Cov.:

AF XY:

0.0307

AC XY:

8485

AN XY:

276060

show subpopulations

Gnomad4 AFR exome

AF:

0.00644

Gnomad4 AMR exome

AF:

0.0187

Gnomad4 ASJ exome

AF:

0.0241

Gnomad4 EAS exome

AF:

0.0000707

Gnomad4 SAS exome

AF:

0.0144

Gnomad4 FIN exome

AF:

0.0865

Gnomad4 NFE exome

AF:

0.0360

Gnomad4 OTH exome

AF:

0.0292

GnomAD4 genome

AF:

0.0278

AC:

4239

AN:

152272

Hom.:

115

Cov.:

AF XY:

0.0297

AC XY:

2210

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.00671

Gnomad4 AMR

AF:

0.0240

Gnomad4 ASJ

AF:

0.0242

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0141

Gnomad4 FIN

AF:

0.0901

Gnomad4 NFE

AF:

0.0355

Gnomad4 OTH

AF:

0.0270

Alfa

AF:

0.0335

Hom.:

Bravo

AF:

0.0223

Asia WGS

AF:

0.00751

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.8

DANN

Benign

0.70

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over