rs234338

chr19-40036831-C-Achr19-40036831-C-T

Variant summary

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

The NM_001005851.3(ZNF780B):c.233-205G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0967 in 151,390 control chromosomes in the GnomAD database, including 2,089 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 0.097 (2089 hom., cov: 32)
• Consequence: ZNF780B NM_001005851.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884

Genes affected

ZNF780B (HGNC:33109): (zinc finger protein 780B) Predicted to enable DNA-binding transcription activator 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 active 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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF780B	NM_001005851.3	c.233-205G>T		intron_variant		ENST00000434248.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF780B	ENST00000434248.6	c.233-205G>T		intron_variant		5	NM_001005851.3	P1
ZNF780B	ENST00000221355.10	c.-212-205G>T		intron_variant		2
ZNF780B	ENST00000598845.5	c.205-205G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0965 AC: 14598 AN: 151298 Hom.: 2082 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0240

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.000386

Gnomad MID AF: 0.0449

Gnomad NFE AF: 0.00741

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0967 AC: 14645 AN: 151390 Hom.: 2089 Cov.: 32 AF XY: 0.0948 AC XY: 7010 AN XY: 73930

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.0392

Gnomad4 ASJ AF: 0.0240

Gnomad4 EAS AF: 0.0113

Gnomad4 SAS AF: 0.0533

Gnomad4 FIN AF: 0.000386

Gnomad4 NFE AF: 0.00741

Gnomad4 OTH AF: 0.0721

Alfa AF: 0.0440 Hom.: 132

Bravo AF: 0.109

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	13
Dann	Benign	0.49

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

Other links and lift over

dbSNP: rs234338; hg19: chr19-40542738;