6-28888795-A-T

Variant names:

• chr6-28888795-A-T
• rs169679
• ENST00000419323.1:n.*37T>A

Variant summary

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

The ENST00000419323.1(ZNF90P2):​n.*37T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,122 control chromosomes in the GnomAD database, including 31,376 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 0.62 (31376 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ZNF90P2 ENST00000419323.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586
• Publications: 13 publications found

Genes affected

ZNF90P2 (HGNC:21687): (zinc finger protein 90 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF90P2	ENST00000419323.1	n.*37T>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94132 AN: 152004 Hom.: 31318 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.628

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.619 AC: 94235 AN: 152122 Hom.: 31376 Cov.: 32 AF XY: 0.616 AC XY: 45788 AN XY: 74354

African (AFR) AF: 0.872 AC: 36224 AN: 41540

American (AMR) AF: 0.587 AC: 8965 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2063 AN: 3470

East Asian (EAS) AF: 0.657 AC: 3401 AN: 5178

South Asian (SAS) AF: 0.627 AC: 3023 AN: 4822

European-Finnish (FIN) AF: 0.421 AC: 4446 AN: 10562

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34050 AN: 67964

Other (OTH) AF: 0.621 AC: 1308 AN: 2106

Alfa AF: 0.559 Hom.: 3129

Bravo AF: 0.648

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.18
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs169679; hg19: chr6-28856572;