18-48105018-C-T

Variant names:

• chr18-48105018-C-T
• rs9947627
• NM_001318841.2:c.-16-63895G>A

Variant summary

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

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318841.2. 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
	ZBTB7C	NM_001318841.2	MANE Select	c.-16-63895G>A		intron	N/A	NP_001305770.1
	ZBTB7C	NM_001039360.3		c.-17+31989G>A		intron	N/A	NP_001034449.1
	ZBTB7C	NM_001371284.1		c.-17+60113G>A		intron	N/A	NP_001358213.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB7C	ENST00000590800.6	TSL:1 MANE Select	c.-16-63895G>A		intron	N/A	ENSP00000467877.1
	ZBTB7C	ENST00000535628.6	TSL:1	c.-17+31989G>A		intron	N/A	ENSP00000439781.1
	ZBTB7C	ENST00000586438.5	TSL:1	c.-17+60113G>A		intron	N/A	ENSP00000468254.1

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

African (AFR) AF: 0.841 AC: 34909 AN: 41532

American (AMR) AF: 0.742 AC: 11350 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2563 AN: 3468

East Asian (EAS) AF: 0.835 AC: 4327 AN: 5180

South Asian (SAS) AF: 0.746 AC: 3598 AN: 4824

European-Finnish (FIN) AF: 0.724 AC: 7677 AN: 10602

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44327 AN: 67980

Other (OTH) AF: 0.694 AC: 1468 AN: 2114

Alfa AF: 0.674 Hom.: 56770

Bravo AF: 0.735

Asia WGS AF: 0.796 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.019
DANN	Benign	0.42
PhyloP100		-2.6
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: rs9947627; hg19: chr18-45631389;