Variant rs1542313 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000358738.3(ZBTB1):c.*1423A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,108 control chromosomes in the GnomAD database, including 20,076 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 0.51 ( 20012 hom., cov: 31)

Exomes 𝑓: 0.64 ( 64 hom. )

Consequence

ZBTB1
ENST00000358738.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.368

Variant links:

Genes affected

ZBTB1 (HGNC:20259): (zinc finger and BTB domain containing 1) Enables K63-linked polyubiquitin modification-dependent protein binding activity; protein heterodimerization activity; and protein homodimerization activity. Involved in several processes, including cellular response to UV; nucleobase-containing compound biosynthetic process; and protein homooligomerization. Located in centrosome; nuclear body; and nuclear membrane. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB1 links:

HSPA2-AS1 (HGNC:55433): (HSPA2 and ZBTB1 antisense RNA 1)

HSPA2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSPA2-AS1	NR_110550.1 linkuse as main transcript	n.53-751T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	UniProt
ZBTB1	ENST00000358738.3 linkuse as main transcript	c.*1423A>C	3_prime_UTR_variant	3/3	1	ENSP00000351587	Q9Y2K1-2
HSPA2-AS1	ENST00000554918.1 linkuse as main transcript	n.53-751T>G	intron_variant, non_coding_transcript_variant		3
HSPA2-AS1	ENST00000648003.1 linkuse as main transcript	n.475-751T>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.509

AC:

77275

AN:

151692

Hom.:

19997

Cov.:

show subpopulations

Gnomad AFR

AF:

0.493

Gnomad AMI

AF:

0.602

Gnomad AMR

AF:

0.583

Gnomad ASJ

AF:

0.448

Gnomad EAS

AF:

0.655

Gnomad SAS

AF:

0.569

Gnomad FIN

AF:

0.612

Gnomad MID

AF:

0.429

Gnomad NFE

AF:

0.474

Gnomad OTH

AF:

0.485

GnomAD4 exome

AF:

0.644

AC:

192

AN:

298

Hom.:

Cov.:

AF XY:

0.642

AC XY:

122

AN XY:

190

show subpopulations

Gnomad4 FIN exome

AF:

0.646

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.509

AC:

77330

AN:

151810

Hom.:

20012

Cov.:

AF XY:

0.518

AC XY:

38447

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.493

Gnomad4 AMR

AF:

0.582

Gnomad4 ASJ

AF:

0.448

Gnomad4 EAS

AF:

0.655

Gnomad4 SAS

AF:

0.567

Gnomad4 FIN

AF:

0.612

Gnomad4 NFE

AF:

0.475

Gnomad4 OTH

AF:

0.488

Alfa

AF:

0.481

Hom.:

11044

Bravo

AF:

0.507

Asia WGS

AF:

0.570

AC:

1970

AN:

3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.60

DANN

Benign

0.62

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over