rs284495

Variant names:

• chr8-104953350-T-C
• rs284495
• ENST00000518180.1:n.197-38274T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-104953350-T-C
• chr8-104953350-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000518180.1(ZFPM2):​n.197-38274T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,890 control chromosomes in the GnomAD database, including 16,001 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 0.44 (16001 hom., cov: 33)
• Consequence: ZFPM2 ENST00000518180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 4 publications found

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 Gene-Disease associations (from GenCC):

• 46,XY sex reversal 9

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• diaphragmatic hernia 3

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P
• tetralogy of fallot

  Inheritance: Unknown, AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• 46,XY partial gonadal dysgenesis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000518180.1	n.197-38274T>C		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66602 AN: 151772 Hom.: 15956 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.439 AC: 66704 AN: 151890 Hom.: 16001 Cov.: 33 AF XY: 0.444 AC XY: 32973 AN XY: 74208

African (AFR) AF: 0.627 AC: 26012 AN: 41460

American (AMR) AF: 0.402 AC: 6116 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2179 AN: 5130

South Asian (SAS) AF: 0.278 AC: 1340 AN: 4820

European-Finnish (FIN) AF: 0.539 AC: 5704 AN: 10576

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22831 AN: 67894

Other (OTH) AF: 0.401 AC: 846 AN: 2110

Alfa AF: 0.370 Hom.: 8293

Bravo AF: 0.437

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.40
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs284495; hg19: chr8-105965578;