rs990072

chr18-5290199-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001243702.2(ZBTB14):c.*659A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,958 control chromosomes in the GnomAD database, including 26,779 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 0.59 (26771 hom., cov: 32)
  • Exomes 𝑓: 0.57 (8 hom.)
• Consequence: ZBTB14 NM_001243702.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566

Genes affected

ZBTB14 (HGNC:12860): (zinc finger and BTB domain containing 14) Enables DNA-binding transcription factor activity and transcription cis-regulatory region binding activity. Involved in negative regulation of transcription, DNA-templated. Located in aggresome; cytosol; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

LINC00667 (HGNC:27906): (long intergenic non-protein coding RNA 667)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB14	NM_001243702.2	c.*659A>G		3_prime_UTR_variant	4/4	ENST00000651870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB14	ENST00000651870.1	c.*659A>G		3_prime_UTR_variant	4/4		NM_001243702.2	P1
LINC00667	ENST00000669574.2	n.1211T>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89444 AN: 151800 Hom.: 26724 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.557

GnomAD4 exome AF: 0.571 AC: 24 AN: 42 Hom.: 8 Cov.: 0 AF XY: 0.583 AC XY: 14 AN XY: 24

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.528

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.589 AC: 89547 AN: 151916 Hom.: 26771 Cov.: 32 AF XY: 0.592 AC XY: 43976 AN XY: 74244

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.562

Alfa AF: 0.547 Hom.: 22766

Bravo AF: 0.592

Asia WGS AF: 0.720 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs990072; hg19: chr18-5290198;