chr3-141377894-C-T

Variant names:

• chr3-141377894-C-T
• rs9822195
• NM_001376113.1:c.-234-3531C>T

Variant summary

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

The NM_001376113.1(ZBTB38):​c.-234-3531C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,066 control chromosomes in the GnomAD database, including 7,945 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 0.31 (7945 hom., cov: 32)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 13 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001376113.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	NM_001376113.1	MANE Select	c.-234-3531C>T		intron	N/A	NP_001363042.1	Q8NAP3
	ZBTB38	NM_001080412.3		c.-479-3531C>T		intron	N/A	NP_001073881.2	Q8NAP3
	ZBTB38	NM_001376112.1		c.-234-3531C>T		intron	N/A	NP_001363041.1	Q8NAP3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	ENST00000321464.7	TSL:6 MANE Select	c.-234-3531C>T		intron	N/A	ENSP00000372635.5	Q8NAP3
	ZBTB38	ENST00000509842.5	TSL:1	c.-479-3531C>T		intron	N/A	ENSP00000426931.1	D6RE69
	ZBTB38	ENST00000507657.1	TSL:1	n.391-3531C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47291 AN: 151946 Hom.: 7933 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.311 AC: 47332 AN: 152066 Hom.: 7945 Cov.: 32 AF XY: 0.304 AC XY: 22567 AN XY: 74330

African (AFR) AF: 0.353 AC: 14631 AN: 41458

American (AMR) AF: 0.198 AC: 3018 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3470

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5180

South Asian (SAS) AF: 0.178 AC: 862 AN: 4832

European-Finnish (FIN) AF: 0.362 AC: 3827 AN: 10566

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22996 AN: 67964

Other (OTH) AF: 0.267 AC: 564 AN: 2112

Alfa AF: 0.317 Hom.: 21616

Bravo AF: 0.300

Asia WGS AF: 0.100 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.45
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs9822195; hg19: chr3-141096736;