rs1582874

Variant names:

• chr3-141396377-T-A
• rs1582874
• ENST00000509842.5:c.-232T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-141396377-T-A
• chr3-141396377-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001080412.3(ZBTB38):​c.-232T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZBTB38 NM_001080412.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 29 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080412.3. 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.-105-7550T>A		intron	N/A	NP_001363042.1	Q8NAP3
	ZBTB38	NM_001080412.3		c.-232T>A		5_prime_UTR	Exon 6 of 8	NP_001073881.2	Q8NAP3
	ZBTB38	NM_001376114.1		c.-232T>A		5_prime_UTR	Exon 5 of 7	NP_001363043.1	Q8NAP3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB38	ENST00000509842.5	TSL:1	c.-232T>A		5_prime_UTR	Exon 6 of 8	ENSP00000426931.1	D6RE69
	ZBTB38	ENST00000321464.7	TSL:6 MANE Select	c.-105-7550T>A		intron	N/A	ENSP00000372635.5	Q8NAP3
	ZBTB38	ENST00000509883.5	TSL:1	c.-105-7550T>A		intron	N/A	ENSP00000424254.1	D6RBC4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2794 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1864

African (AFR) AF: 0.00 AC: 0 AN: 58

American (AMR) AF: 0.00 AC: 0 AN: 140

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 72

East Asian (EAS) AF: 0.00 AC: 0 AN: 200

South Asian (SAS) AF: 0.00 AC: 0 AN: 148

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 58

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 18

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1972

Other (OTH) AF: 0.00 AC: 0 AN: 128

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 2239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-1.7

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1582874;

hg19: chr3-141115219;