rs4801298

chr19-56195679-G-Achr19-56195679-G-Cchr19-56195679-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080456.5(ZSCAN5B):c.-128+2055C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 151,400 control chromosomes in the GnomAD database, including 36,545 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 0.69 (36545 hom., cov: 30)
• Consequence: ZSCAN5B NM_001080456.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

ZSCAN5B (HGNC:34246): (zinc finger and SCAN domain containing 5B) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSCAN5B	NM_001080456.5	c.-128+2055C>T		intron_variant		ENST00000586855.7
ZSCAN5B	NM_001385638.1	c.-3+2055C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN5B	ENST00000586855.7	c.-128+2055C>T		intron_variant		5	NM_001080456.5	P1
ZSCAN5B	ENST00000587032.2	c.-63+2055C>T		intron_variant		5
ZSCAN5B	ENST00000589938.5	c.-3+2055C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.694 AC: 104953 AN: 151286 Hom.: 36500 Cov.: 30

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.694 AC: 105058 AN: 151400 Hom.: 36545 Cov.: 30 AF XY: 0.689 AC XY: 50979 AN XY: 73968

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.686

Alfa AF: 0.684 Hom.: 15946

Bravo AF: 0.695

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.50
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4801298; hg19: chr19-56707048;