3-141374443-T-C

Variant names:

• chr3-141374443-T-C
• rs7624084
• NM_001376113.1:c.-235+4497T>C

Variant summary

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

The NM_001376113.1(ZBTB38):​c.-235+4497T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,928 control chromosomes in the GnomAD database, including 23,441 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 0.53 (23441 hom., cov: 31)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 36 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB38	NM_001376113.1	c.-235+4497T>C		intron_variant	Intron 2 of 5	ENST00000321464.7	NP_001363042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000321464.7	c.-235+4497T>C		intron_variant	Intron 2 of 5	6	NM_001376113.1	ENSP00000372635.5

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80272 AN: 151810 Hom.: 23404 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.529 AC: 80373 AN: 151928 Hom.: 23441 Cov.: 31 AF XY: 0.523 AC XY: 38827 AN XY: 74274

African (AFR) AF: 0.799 AC: 33100 AN: 41450

American (AMR) AF: 0.450 AC: 6865 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1464 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1712 AN: 5146

South Asian (SAS) AF: 0.367 AC: 1763 AN: 4804

European-Finnish (FIN) AF: 0.431 AC: 4546 AN: 10556

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29543 AN: 67932

Other (OTH) AF: 0.467 AC: 983 AN: 2104

Alfa AF: 0.458 Hom.: 40705

Bravo AF: 0.540

Asia WGS AF: 0.346 AC: 1202 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	1.1
DANN	Benign	0.71
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7624084; hg19: chr3-141093285;