NM_001005851.3:c.233-205G>T

Variant names:

• chr19-40036831-C-A
• rs234338
• NM_001005851.3:c.233-205G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005851.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF780B	NM_001005851.3	MANE Select	c.233-205G>T		intron	N/A	NP_001005851.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF780B	ENST00000434248.6	TSL:5 MANE Select	c.233-205G>T		intron	N/A	ENSP00000391641.1
	ZNF780B	ENST00000221355.10	TSL:2	c.-212-205G>T		intron	N/A	ENSP00000221355.6
	ZNF780B	ENST00000598845.5	TSL:3	c.205-205G>T		intron	N/A	ENSP00000471669.1

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

African (AFR) AF: 0.315 AC: 12984 AN: 41242

American (AMR) AF: 0.0392 AC: 597 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.0240 AC: 83 AN: 3464

East Asian (EAS) AF: 0.0113 AC: 58 AN: 5146

South Asian (SAS) AF: 0.0533 AC: 255 AN: 4788

European-Finnish (FIN) AF: 0.000386 AC: 4 AN: 10364

Middle Eastern (MID) AF: 0.0347 AC: 10 AN: 288

European-Non Finnish (NFE) AF: 0.00741 AC: 503 AN: 67880

Other (OTH) AF: 0.0721 AC: 151 AN: 2094

Alfa AF: 0.0551 Hom.: 170

Bravo AF: 0.109

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.49
PhyloP100		-0.88
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: rs234338; hg19: chr19-40542738;