chr8-105561691-C-T

Position:

• chr8-105561691-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_012082.4(ZFPM2):​c.420+210C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,932 control chromosomes in the GnomAD database, including 13,508 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.42 (13508 hom., cov: 32)
• Consequence: ZFPM2 NM_012082.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.70

Genes affected

ZFPM2 (HGNC:16700): (zinc finger protein, FOG family member 2) The zinc finger protein encoded by this gene is a widely expressed member of the FOG family of transcription factors. The family members modulate the activity of GATA family proteins, which are important regulators of hematopoiesis and cardiogenesis in mammals. It has been demonstrated that the protein can both activate and down-regulate expression of GATA-target genes, suggesting different modulation in different promoter contexts. A related mRNA suggests an alternatively spliced product but this information is not yet fully supported by the sequence. [provided by RefSeq, Jul 2008]

ZFPM2-AS1 (HGNC:50698): (ZFPM2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BP6: Variant 8-105561691-C-T is Benign according to our data. Variant chr8-105561691-C-T is described in ClinVar as [Benign]. Clinvar id is 1227492.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFPM2	NM_012082.4	c.420+210C>T		intron_variant		ENST00000407775.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFPM2	ENST00000407775.7	c.420+210C>T		intron_variant		1	NM_012082.4	P1

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64084 AN: 151816 Hom.: 13510 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.422 AC: 64096 AN: 151932 Hom.: 13508 Cov.: 32 AF XY: 0.416 AC XY: 30891 AN XY: 74248

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.438

Alfa AF: 0.436 Hom.: 2958

Bravo AF: 0.419

Asia WGS AF: 0.482 AC: 1673 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 13, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Benign	0.44

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: rs12216772; hg19: chr8-106573919;