ENST00000532116.3:n.493-789C>T

Variant names:

• chr11-130392706-C-T
• rs11606448
• ENST00000532116.3:n.493-789C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532116.3(ZBTB44-DT):​n.493-789C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,246 control chromosomes in the GnomAD database, including 1,991 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 0.15 (1991 hom., cov: 34)
• Consequence: ZBTB44-DT ENST00000532116.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 5 publications found

Genes affected

ZBTB44-DT (HGNC:54265): (ZBTB44 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB44-DT	NR_148980.1	n.273-789C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB44-DT	ENST00000532116.3	n.493-789C>T		intron_variant	Intron 4 of 5	3
ZBTB44-DT	ENST00000602376.6	n.281-789C>T		intron_variant	Intron 2 of 5	5
ZBTB44-DT	ENST00000616197.2	n.244-789C>T		intron_variant	Intron 2 of 6	3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22550 AN: 152128 Hom.: 1991 Cov.: 34

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.148 AC: 22549 AN: 152246 Hom.: 1991 Cov.: 34 AF XY: 0.147 AC XY: 10913 AN XY: 74430

African (AFR) AF: 0.0791 AC: 3287 AN: 41572

American (AMR) AF: 0.213 AC: 3265 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3470

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5168

South Asian (SAS) AF: 0.0786 AC: 379 AN: 4822

European-Finnish (FIN) AF: 0.161 AC: 1712 AN: 10610

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12632 AN: 67986

Other (OTH) AF: 0.160 AC: 339 AN: 2116

Alfa AF: 0.175 Hom.: 3243

Bravo AF: 0.151

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.68
PhyloP100		0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11606448; hg19: chr11-130262601;