3-141420488-G-A

Variant names:

• chr3-141420488-G-A
• rs6785073
• NM_001376113.1:c.-1+16457G>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+16457G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,112 control chromosomes in the GnomAD database, including 5,503 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 0.24 (5503 hom., cov: 32)
• Consequence: ZBTB38 NM_001376113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 15 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	NM_001376113.1	MANE Select	c.-1+16457G>A		intron	N/A	NP_001363042.1
	ZBTB38	NM_001080412.3		c.-1+16457G>A		intron	N/A	NP_001073881.2
	ZBTB38	NM_001350099.2		c.-190-11664G>A		intron	N/A	NP_001337028.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	ENST00000321464.7	TSL:6 MANE Select	c.-1+16457G>A		intron	N/A	ENSP00000372635.5
	ZBTB38	ENST00000509883.5	TSL:1	c.-1+16457G>A		intron	N/A	ENSP00000424254.1
	ZBTB38	ENST00000509842.5	TSL:1	c.-1+16457G>A		intron	N/A	ENSP00000426931.1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37029 AN: 151994 Hom.: 5504 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.243 AC: 37029 AN: 152112 Hom.: 5503 Cov.: 32 AF XY: 0.237 AC XY: 17649 AN XY: 74362

African (AFR) AF: 0.123 AC: 5093 AN: 41518

American (AMR) AF: 0.166 AC: 2533 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5186

South Asian (SAS) AF: 0.153 AC: 736 AN: 4822

European-Finnish (FIN) AF: 0.362 AC: 3827 AN: 10568

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22902 AN: 67958

Other (OTH) AF: 0.218 AC: 460 AN: 2110

Alfa AF: 0.301 Hom.: 8943

Bravo AF: 0.223

Asia WGS AF: 0.0740 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.52
PhyloP100		1.5
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: rs6785073; hg19: chr3-141139330;