rs16872085

Positions:

• chr8-104945312-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 0.0788 in 152,064 control chromosomes in the GnomAD database, including 589 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 0.079 (589 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.104945312A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000518180.1	n.197-46312A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 11989 AN: 151946 Hom.: 589 Cov.: 32

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0680

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0809

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.0788 AC: 11982 AN: 152064 Hom.: 589 Cov.: 32 AF XY: 0.0794 AC XY: 5903 AN XY: 74320

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.0687

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0680

Gnomad4 NFE AF: 0.0809

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.0876 Hom.: 1239

Bravo AF: 0.0799

Asia WGS AF: 0.138 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16872085; hg19: chr8-105957540;