18-48105018-C-T

Variant summary

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

The NM_001318841.2(ZBTB7C):c.-16-63895G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,200 control chromosomes in the GnomAD database, including 41,031 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 0.73 (41031 hom., cov: 33)
• Consequence: ZBTB7C NM_001318841.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

Genes affected

ZBTB7C (HGNC:31700): (zinc finger and BTB domain containing 7C) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of cell population proliferation. 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB7C	NM_001318841.2	c.-16-63895G>A		intron_variant		ENST00000590800.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB7C	ENST00000590800.6	c.-16-63895G>A		intron_variant		1	NM_001318841.2	P1

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110917 AN: 152082 Hom.: 40981 Cov.: 33

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.729 AC: 111025 AN: 152200 Hom.: 41031 Cov.: 33 AF XY: 0.734 AC XY: 54574 AN XY: 74400

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.694

Alfa AF: 0.673 Hom.: 47797

Bravo AF: 0.735

Asia WGS AF: 0.796 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.019
Dann	Benign	0.42

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: rs9947627; hg19: chr18-45631389;