rs990072

Variant names:

• chr18-5290199-T-C
• rs990072
• NM_001243702.2:c.*659A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZBTB14	NM_001243702.2	c.*659A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000651870.1	NP_001230631.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB14	ENST00000651870.1	c.*659A>G		3_prime_UTR_variant	Exon 4 of 4		NM_001243702.2	ENSP00000499212.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.528 AC: 19 AN: 36

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.647 AC: 26782 AN: 41406

American (AMR) AF: 0.613 AC: 9364 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2038 AN: 3466

East Asian (EAS) AF: 0.788 AC: 4068 AN: 5162

South Asian (SAS) AF: 0.664 AC: 3202 AN: 4824

European-Finnish (FIN) AF: 0.540 AC: 5683 AN: 10526

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36592 AN: 67934

Other (OTH) AF: 0.562 AC: 1186 AN: 2110

Alfa AF: 0.552 Hom.: 30063

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
PhyloP100		-0.57
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: rs990072; hg19: chr18-5290198;