NM_001376113.1:c.1-18730C>T

Variant names:

• chr3-141423659-C-T
• rs16851419
• NM_001376113.1:c.1-18730C>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.1-18730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0441 in 152,116 control chromosomes in the GnomAD database, including 260 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 0.044 (260 hom., cov: 32)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0926 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.1-18730C>T		intron	N/A	NP_001363042.1	Q8NAP3
	ZBTB38	NM_001080412.3		c.1-18730C>T		intron	N/A	NP_001073881.2	Q8NAP3
	ZBTB38	NM_001350099.2		c.-190-8493C>T		intron	N/A	NP_001337028.1	Q8NAP3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	ENST00000321464.7	TSL:6 MANE Select	c.1-18730C>T		intron	N/A	ENSP00000372635.5	Q8NAP3
	ZBTB38	ENST00000509883.5	TSL:1	c.1-18730C>T		intron	N/A	ENSP00000424254.1	D6RBC4
	ZBTB38	ENST00000509842.5	TSL:1	c.1-18730C>T		intron	N/A	ENSP00000426931.1	D6RE69

Frequencies

GnomAD3 genomes AF: 0.0440 AC: 6686 AN: 151998 Hom.: 261 Cov.: 32

Gnomad AFR AF: 0.0766

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0888

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.00756

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0441 AC: 6703 AN: 152116 Hom.: 260 Cov.: 32 AF XY: 0.0458 AC XY: 3408 AN XY: 74350

African (AFR) AF: 0.0768 AC: 3186 AN: 41492

American (AMR) AF: 0.0967 AC: 1476 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3470

East Asian (EAS) AF: 0.0888 AC: 460 AN: 5178

South Asian (SAS) AF: 0.0479 AC: 231 AN: 4822

European-Finnish (FIN) AF: 0.00756 AC: 80 AN: 10576

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0157 AC: 1065 AN: 67996

Other (OTH) AF: 0.0455 AC: 96 AN: 2108

Alfa AF: 0.0332 Hom.: 276

Bravo AF: 0.0535

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism

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: rs16851419; hg19: chr3-141142501;