Genetic Variant IQCB2P:n.28012442G>T (chr6-28012442-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The variant allele was found at a frequency of 0.00000296 in 337,302 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000030 ( 0 hom. )

Consequence

IQCB2P
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.849

Publications

0 publications found

Variant links:

Genes affected

IQCB2P (HGNC:17727): (IQ motif containing B2 pseudogene)

IQCB2P links:

ZSCAN16-AS1 (HGNC:48982): (ZSCAN16 antisense RNA 1)

ZSCAN16-AS1 links:

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ACMG classification

Classification was made for transcript

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=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IQCB2P		n.28012442G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ZSCAN16-AS1	ENST00000716089.1 link	n.224-3434C>A	intron_variant	Intron 2 of 2
ZSCAN16-AS1	ENST00000716090.1 link	n.311-3434C>A	intron_variant	Intron 3 of 3
ZSCAN16-AS1	ENST00000733323.1 link	n.223-3434C>A	intron_variant	Intron 2 of 2
IQCB2P	ENST00000401788.2 link	n.*87G>T	downstream_gene_variant		6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000296

AC:

AN:

337302

Hom.:

AF XY:

0.00000557

AC XY:

AN XY:

179674

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

9816

American (AMR)

AF:

0.00

AC:

AN:

16866

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10208

East Asian (EAS)

AF:

0.00

AC:

AN:

20258

South Asian (SAS)

AF:

0.00

AC:

AN:

39554

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20024

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1908

European-Non Finnish (NFE)

AF:

0.00000501

AC:

AN:

199438

Other (OTH)

AF:

0.00

AC:

AN:

19230

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.225

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.58

(source)

DANN

Benign

0.72

PhyloP100

-0.85

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over