chr3-141415118-G-A

Variant names:

• chr3-141415118-G-A
• rs13091182
• NM_001376113.1:c.-1+11087G>A

Variant summary

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

The NM_001376113.1(ZBTB38):​c.-1+11087G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 148,844 control chromosomes in the GnomAD database, including 5,502 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 0.25 (5502 hom., cov: 30)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918
• Publications: 19 publications found

Genes affected

ZBTB38 (HGNC:26636): (zinc finger and BTB domain containing 38) The protein encoded by this gene is a zinc finger transcriptional activator that binds methylated DNA. The encoded protein can form homodimers or heterodimers through the zinc finger domains. In mouse, inhibition of this protein has been associated with apoptosis in some cell types. [provided by RefSeq, Jun 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB38	NM_001376113.1	c.-1+11087G>A		intron_variant	Intron 5 of 5	ENST00000321464.7	NP_001363042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000321464.7	c.-1+11087G>A		intron_variant	Intron 5 of 5	6	NM_001376113.1	ENSP00000372635.5

Frequencies

GnomAD3 genomes AF: 0.249 AC: 36969 AN: 148734 Hom.: 5503 Cov.: 30

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.284

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.248 AC: 36969 AN: 148844 Hom.: 5502 Cov.: 30 AF XY: 0.243 AC XY: 17597 AN XY: 72556

African (AFR) AF: 0.127 AC: 5113 AN: 40280

American (AMR) AF: 0.169 AC: 2539 AN: 14986

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1094 AN: 3436

East Asian (EAS) AF: 0.00329 AC: 16 AN: 4864

South Asian (SAS) AF: 0.150 AC: 699 AN: 4666

European-Finnish (FIN) AF: 0.369 AC: 3823 AN: 10354

Middle Eastern (MID) AF: 0.291 AC: 75 AN: 258

European-Non Finnish (NFE) AF: 0.341 AC: 22876 AN: 67066

Other (OTH) AF: 0.224 AC: 459 AN: 2048

Alfa AF: 0.269 Hom.: 8128

Bravo AF: 0.223

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.4
DANN	Benign	0.79
PhyloP100		0.92
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: rs13091182; hg19: chr3-141133960;