8-104925183-A-G

Position:

• chr8-104925183-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0636 in 152,140 control chromosomes in the GnomAD database, including 571 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 0.064 (571 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.104925183A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000518180.1	n.197-66441A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 9651 AN: 152022 Hom.: 567 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0854

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0636 AC: 9679 AN: 152140 Hom.: 571 Cov.: 32 AF XY: 0.0675 AC XY: 5017 AN XY: 74378

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0855

Gnomad4 ASJ AF: 0.0253

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.0143

Gnomad4 OTH AF: 0.0558

Alfa AF: 0.0381 Hom.: 65

Bravo AF: 0.0673

Asia WGS AF: 0.112 AC: 390 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	0.14
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505068; hg19: chr8-105937411;