chr14-50704161-T-G

Variant names:

• chr14-50704161-T-G
• rs8020441

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 0.235 in 152,066 control chromosomes in the GnomAD database, including 4,390 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 0.24 (4390 hom., cov: 32)
• Consequence: ZFP64P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 9 publications found

Genes affected

ZFP64P1 (HGNC:19820): (ZFP64 zinc finger protein pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFP64P1		n.50704161T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFP64P1	ENST00000553836.2	n.*182A>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35735 AN: 151948 Hom.: 4389 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.235 AC: 35770 AN: 152066 Hom.: 4390 Cov.: 32 AF XY: 0.232 AC XY: 17243 AN XY: 74334

African (AFR) AF: 0.311 AC: 12914 AN: 41468

American (AMR) AF: 0.176 AC: 2682 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1090 AN: 3464

East Asian (EAS) AF: 0.169 AC: 873 AN: 5176

South Asian (SAS) AF: 0.206 AC: 995 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2088 AN: 10576

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14425 AN: 67970

Other (OTH) AF: 0.224 AC: 472 AN: 2110

Alfa AF: 0.224 Hom.: 10492

Bravo AF: 0.257

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.31
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs8020441; hg19: chr14-51170879;