rs4801298

Variant names:

• chr19-56195679-G-A
• rs4801298
• NM_001080456.5:c.-128+2055C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-56195679-G-A
• chr19-56195679-G-C
• chr19-56195679-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZSCAN5B	NM_001080456.5	c.-128+2055C>T		intron_variant	Intron 1 of 4	ENST00000586855.7	NP_001073925.2
ZSCAN5B	NM_001385638.1	c.-3+2055C>T		intron_variant	Intron 1 of 4		NP_001372567.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN5B	ENST00000586855.7	c.-128+2055C>T		intron_variant	Intron 1 of 4	5	NM_001080456.5	ENSP00000466072.2
ZSCAN5B	ENST00000589938.5	c.-3+2055C>T		intron_variant	Intron 1 of 2	5		ENSP00000465118.1
ZSCAN5B	ENST00000587032.2	c.-63+2055C>T		intron_variant	Intron 1 of 3	5		ENSP00000468660.2

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

African (AFR) AF: 0.734 AC: 30276 AN: 41240

American (AMR) AF: 0.679 AC: 10339 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2579 AN: 3466

East Asian (EAS) AF: 0.666 AC: 3410 AN: 5120

South Asian (SAS) AF: 0.659 AC: 3164 AN: 4802

European-Finnish (FIN) AF: 0.641 AC: 6721 AN: 10484

Middle Eastern (MID) AF: 0.810 AC: 235 AN: 290

European-Non Finnish (NFE) AF: 0.683 AC: 46268 AN: 67776

Other (OTH) AF: 0.686 AC: 1435 AN: 2092

Alfa AF: 0.685 Hom.: 17777

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
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4801298; hg19: chr19-56707048;