3-141443286-C-G

Variant names:

• chr3-141443286-C-G
• rs62282002
• NM_001376113.1:c.898C>G

Variant summary

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

The NM_001376113.1(ZBTB38):​c.898C>G​(p.Pro300Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0973 in 1,614,158 control chromosomes in the GnomAD database, including 9,479 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.085 (895 hom., cov: 32)
  • Exomes 𝑓: 0.099 (8584 hom.)
• Consequence: ZBTB38 NM_001376113.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 17 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]

ENSG00000288585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=0.0018695891).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB38	NM_001376113.1	c.898C>G	p.Pro300Ala	missense_variant	Exon 6 of 6	ENST00000321464.7	NP_001363042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB38	ENST00000321464.7	c.898C>G	p.Pro300Ala	missense_variant	Exon 6 of 6	6	NM_001376113.1	ENSP00000372635.5

Frequencies

GnomAD3 genomes AF: 0.0852 AC: 12960 AN: 152156 Hom.: 898 Cov.: 32

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.0874

GnomAD2 exomes AF: 0.121 AC: 30080 AN: 249372 AF XY: 0.117

Gnomad AFR exome AF: 0.0160

Gnomad AMR exome AF: 0.237

Gnomad ASJ exome AF: 0.0810

Gnomad EAS exome AF: 0.256

Gnomad FIN exome AF: 0.0864

Gnomad NFE exome AF: 0.0912

Gnomad OTH exome AF: 0.100

GnomAD4 exome AF: 0.0985 AC: 144042 AN: 1461884 Hom.: 8584 Cov.: 33 AF XY: 0.0981 AC XY: 71354 AN XY: 727240

African (AFR) AF: 0.0144 AC: 482 AN: 33480

American (AMR) AF: 0.232 AC: 10398 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0812 AC: 2121 AN: 26136

East Asian (EAS) AF: 0.276 AC: 10968 AN: 39700

South Asian (SAS) AF: 0.114 AC: 9808 AN: 86258

European-Finnish (FIN) AF: 0.0845 AC: 4515 AN: 53414

Middle Eastern (MID) AF: 0.0837 AC: 483 AN: 5768

European-Non Finnish (NFE) AF: 0.0897 AC: 99769 AN: 1112008

Other (OTH) AF: 0.0910 AC: 5498 AN: 60396

GnomAD4 genome AF: 0.0850 AC: 12943 AN: 152274 Hom.: 895 Cov.: 32 AF XY: 0.0899 AC XY: 6690 AN XY: 74450

African (AFR) AF: 0.0173 AC: 719 AN: 41554

American (AMR) AF: 0.190 AC: 2901 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0873 AC: 303 AN: 3470

East Asian (EAS) AF: 0.246 AC: 1273 AN: 5176

South Asian (SAS) AF: 0.112 AC: 539 AN: 4830

European-Finnish (FIN) AF: 0.0992 AC: 1051 AN: 10596

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0866 AC: 5894 AN: 68026

Other (OTH) AF: 0.0865 AC: 183 AN: 2116

Alfa AF: 0.0815 Hom.: 466

Bravo AF: 0.0880

TwinsUK AF: 0.0850 AC: 315

ALSPAC AF: 0.0942 AC: 363

ESP6500AA AF: 0.0195 AC: 74

ESP6500EA AF: 0.0887 AC: 730

ExAC AF: 0.115 AC: 13902

Asia WGS AF: 0.125 AC: 432 AN: 3478

EpiCase AF: 0.0832

EpiControl AF: 0.0804

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
BayesDel_addAF	Benign	-0.66	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	16
DANN	Benign	0.44
DEOGEN2	Benign	0.011	T;.;T;T;T;T
Eigen	Benign	-0.21
Eigen_PC	Benign	-0.054
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Benign	0.58	T;T;.;.;.;T
MetaRNN	Benign	0.0019	T;T;T;T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Uncertain	2.3	.;.;M;M;M;M
PhyloP100		1.7
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-0.24	.;N;N;.;N;.
REVEL	Benign	0.047
Sift	Benign	0.27	.;T;T;.;T;.
Sift4G	Benign	0.63	.;T;T;.;T;T
Polyphen		0.10	.;.;B;B;B;B
Vest4		0.088, 0.079, 0.072
MPC		0.45
ClinPred		0.013	T
GERP RS		5.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.027
gMVP		0.22
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: rs62282002; hg19: chr3-141162128; COSMIC: COSV58540734; COSMIC: COSV58540734;