Variant 10-123008776-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001372123.1(IKZF5):c.-280C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 607,124 control chromosomes in the GnomAD database, including 117,738 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 27206 hom., cov: 32)

Exomes 𝑓: 0.62 ( 90532 hom. )

Consequence

IKZF5
NM_001372123.1 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.156

Variant links:

Genes affected

IKZF5 (HGNC:14283): (IKAROS family zinc finger 5) Members of the Ikaros (ZNFN1A1; MIM 603023) family of transcription factors, which includes Pegasus, are expressed in lymphocytes and are implicated in the control of lymphoid development.[supplied by OMIM, Jul 2002]

IKZF5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 10-123008776-G-A is Benign according to our data. Variant chr10-123008776-G-A is described in ClinVar as [Benign]. Clinvar id is 1166420.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IKZF5	NM_001372123.1 linkuse as main transcript	c.-280C>T		5_prime_UTR_variant	1/5	ENST00000368886.10	NP_001359052.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
IKZF5	ENST00000368886.10 linkuse as main transcript	c.-280C>T	5_prime_UTR_variant	1/5	1	NM_001372123.1	ENSP00000357881	P1
IKZF5	ENST00000479103.1 linkuse as main transcript	n.37C>T	non_coding_transcript_exon_variant	1/3	2
IKZF5	ENST00000496605.5 linkuse as main transcript	n.32C>T	non_coding_transcript_exon_variant	1/4	2
IKZF5	ENST00000469821.1 linkuse as main transcript		upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.585

AC:

88778

AN:

151884

Hom.:

27197

Cov.:

show subpopulations

Gnomad AFR

AF:

0.453

Gnomad AMI

AF:

0.693

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.709

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.432

Gnomad FIN

AF:

0.654

Gnomad MID

AF:

0.658

Gnomad NFE

AF:

0.693

Gnomad OTH

AF:

0.612

GnomAD4 exome

AF:

0.615

AC:

280056

AN:

455122

Hom.:

90532

Cov.:

AF XY:

0.609

AC XY:

147218

AN XY:

241582

show subpopulations

Gnomad4 AFR exome

AF:

0.451

Gnomad4 AMR exome

AF:

0.481

Gnomad4 ASJ exome

AF:

0.711

Gnomad4 EAS exome

AF:

0.254

Gnomad4 SAS exome

AF:

0.461

Gnomad4 FIN exome

AF:

0.646

Gnomad4 NFE exome

AF:

0.692

Gnomad4 OTH exome

AF:

0.620

GnomAD4 genome

AF:

0.584

AC:

88825

AN:

152002

Hom.:

27206

Cov.:

AF XY:

0.579

AC XY:

43030

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.453

Gnomad4 AMR

AF:

0.529

Gnomad4 ASJ

AF:

0.709

Gnomad4 EAS

AF:

0.251

Gnomad4 SAS

AF:

0.433

Gnomad4 FIN

AF:

0.654

Gnomad4 NFE

AF:

0.693

Gnomad4 OTH

AF:

0.609

Alfa

AF:

0.629

Hom.:

3718

Bravo

AF:

0.569

Asia WGS

AF:

0.341

AC:

1190

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	This variant is associated with the following publications: (PMID: 17143180) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Deficiency of 2-methylbutyryl-CoA dehydrogenase

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 15, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Benign

0.97

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over