rs977396

Variant names:

• chr8-104980468-G-A
• rs977396
• ENST00000518180.1:n.197-11156G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-104980468-G-A
• chr8-104980468-G-C
• chr8-104980468-G-T

Variant summary

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

The ENST00000518180.1(ZFPM2):​n.197-11156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,128 control chromosomes in the GnomAD database, including 61,424 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 0.90 (61424 hom., cov: 32)
• Consequence: ZFPM2 ENST00000518180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 12 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 = 0.963 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.197-11156G>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136324 AN: 152010 Hom.: 61367 Cov.: 32

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.897 AC: 136438 AN: 152128 Hom.: 61424 Cov.: 32 AF XY: 0.893 AC XY: 66405 AN XY: 74348

African (AFR) AF: 0.971 AC: 40317 AN: 41542

American (AMR) AF: 0.853 AC: 13014 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3056 AN: 3466

East Asian (EAS) AF: 0.835 AC: 4307 AN: 5158

South Asian (SAS) AF: 0.933 AC: 4497 AN: 4818

European-Finnish (FIN) AF: 0.803 AC: 8488 AN: 10576

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59794 AN: 67994

Other (OTH) AF: 0.877 AC: 1853 AN: 2112

Alfa AF: 0.886 Hom.: 260419

Bravo AF: 0.904

Asia WGS AF: 0.871 AC: 3027 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.47
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs977396; hg19: chr8-105992696;