rs285814

Positions:

• chr8-105096256-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.336 in 152,008 control chromosomes in the GnomAD database, including 9,898 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 0.34 (9898 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.20

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.105096256T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFPM2	ENST00000518180.1	n.242+104587T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51121 AN: 151888 Hom.: 9903 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.336 AC: 51124 AN: 152008 Hom.: 9898 Cov.: 32 AF XY: 0.335 AC XY: 24916 AN XY: 74294

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.350

Alfa AF: 0.374 Hom.: 1436

Bravo AF: 0.335

Asia WGS AF: 0.269 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	22
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285814; hg19: chr8-106108484;