chr19-44466713-G-T

Variant names:

• chr19-44466713-G-T
• rs644148

Variant summary

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

The variant allele was found at a frequency of 0.302 in 152,036 control chromosomes in the GnomAD database, including 8,313 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 0.30 (8313 hom., cov: 32)
• Consequence: ZNF285BP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 14 publications found

Genes affected

ZNF285BP (HGNC:33262): (zinc finger protein 285B, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=3.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45863 AN: 151916 Hom.: 8316 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.302 AC: 45857 AN: 152036 Hom.: 8313 Cov.: 32 AF XY: 0.299 AC XY: 22196 AN XY: 74312

African (AFR) AF: 0.107 AC: 4434 AN: 41482

American (AMR) AF: 0.343 AC: 5243 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1239 AN: 3464

East Asian (EAS) AF: 0.156 AC: 810 AN: 5176

South Asian (SAS) AF: 0.422 AC: 2032 AN: 4818

European-Finnish (FIN) AF: 0.300 AC: 3164 AN: 10554

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27619 AN: 67946

Other (OTH) AF: 0.333 AC: 702 AN: 2108

Alfa AF: 0.377 Hom.: 6624

Bravo AF: 0.293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	3.6
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs644148;