rs11606448

Positions:

• chr11-130392706-C-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.273-789C>T variant causes a intron, non coding transcript 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 NR_148980.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

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=-0.9).
• 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/exons	MANE	UniProt
ZBTB44-DT	NR_148980.1	n.273-789C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB44-DT	ENST00000649867.1	n.207-789C>T		intron_variant, non_coding_transcript_variant
ZBTB44-DT	ENST00000532116.3	n.493-789C>T		intron_variant, non_coding_transcript_variant		3
ZBTB44-DT	ENST00000602376.5	n.273-789C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0791

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.00252

Gnomad4 SAS AF: 0.0786

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.160

Alfa AF: 0.176 Hom.: 2538

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11606448; hg19: chr11-130262601;