Variant X-65414981-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000338957.5(ZC3H12B):c.-157+16277C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 111,604 control chromosomes in the GnomAD database, including 2,738 homozygotes. There are 4,421 hemizygotes in GnomAD. 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 0.14 ( 2738 hom., 4421 hem., cov: 23)

Consequence

ZC3H12B
ENST00000338957.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.235

Variant links:

Genes affected

ZC3H12B (HGNC:17407): (zinc finger CCCH-type containing 12B) The protein encoded by this gene belongs to a family of CCCH-type zinc finger proteins that are involved in the proinflammatory activation of macrophages. The exact function of this family member is unknown, but it is thought to function as a ribonuclease. [provided by RefSeq, May 2010]

ZC3H12B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZC3H12B	NM_001010888.4 linkuse as main transcript	c.-157+16277C>T		intron_variant		ENST00000338957.5	NP_001010888.3

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
ZC3H12B	ENST00000338957.5 linkuse as main transcript	c.-157+16277C>T	intron_variant	1	NM_001010888.4	ENSP00000340839	P1	Q5HYM0-1
ZC3H12B	ENST00000696368.1 linkuse as main transcript	c.-252+16328C>T	intron_variant			ENSP00000512583
ZC3H12B	ENST00000617377.1 linkuse as main transcript	n.407+16277C>T	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.143

AC:

15980

AN:

111551

Hom.:

2730

Cov.:

AF XY:

0.130

AC XY:

4389

AN XY:

33791

show subpopulations

Gnomad AFR

AF:

0.488

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0512

Gnomad ASJ

AF:

0.00528

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0262

Gnomad FIN

AF:

0.00247

Gnomad MID

AF:

0.0424

Gnomad NFE

AF:

0.00589

Gnomad OTH

AF:

0.106

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.144

AC:

16032

AN:

111604

Hom.:

2738

Cov.:

AF XY:

0.131

AC XY:

4421

AN XY:

33854

show subpopulations

Gnomad4 AFR

AF:

0.489

Gnomad4 AMR

AF:

0.0513

Gnomad4 ASJ

AF:

0.00528

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0263

Gnomad4 FIN

AF:

0.00247

Gnomad4 NFE

AF:

0.00589

Gnomad4 OTH

AF:

0.106

Alfa

AF:

0.0311

Hom.:

434

Bravo

AF:

0.163

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.6

DANN

Benign

0.69

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