11-130403335-A-T

Position:

• chr11-130403335-A-T

Variant summary

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

The NR_148980.1(ZBTB44-DT):​n.646A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 153,428 control chromosomes in the GnomAD database, including 7,233 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 0.29 (7159 hom., cov: 33)
  • Exomes 𝑓: 0.31 (74 hom.)
• Consequence: ZBTB44-DT NR_148980.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB44-DT	NR_148980.1	n.646A>T		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB44-DT	ENST00000649867.1	n.502A>T		non_coding_transcript_exon_variant	6/6
ZBTB44-DT	ENST00000616197.1	n.91A>T		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44856 AN: 152034 Hom.: 7157 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.289

GnomAD4 exome AF: 0.306 AC: 391 AN: 1276 Hom.: 74 Cov.: 0 AF XY: 0.315 AC XY: 213 AN XY: 676

Gnomad4 AFR exome AF: 0.318

Gnomad4 AMR exome AF: 0.233

Gnomad4 ASJ exome AF: 0.292

Gnomad4 EAS exome AF: 0.0507

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.307

Gnomad4 NFE exome AF: 0.362

Gnomad4 OTH exome AF: 0.257

GnomAD4 genome AF: 0.295 AC: 44872 AN: 152152 Hom.: 7159 Cov.: 33 AF XY: 0.293 AC XY: 21756 AN XY: 74350

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.0311

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.292

Alfa AF: 0.330 Hom.: 4797

Bravo AF: 0.287

Asia WGS AF: 0.149 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	15
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11222084; hg19: chr11-130273230;