19-44110055-C-T

Position:

• chr19-44110055-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592946.1(ZNF225-AS1):​n.325-1718G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,134 control chromosomes in the GnomAD database, including 40,474 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 0.72 (40474 hom., cov: 33)
• Consequence: ZNF225-AS1 ENST00000592946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

Genes affected

ZNF225-AS1 (HGNC:55916): (ZNF225 and ZNF224 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF225-AS1	NR_033341.1	n.363-1718G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF225-AS1	ENST00000592946.1	n.325-1718G>A		intron_variant		1
ZNF225-AS1	ENST00000661725.1	n.363-1718G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109228 AN: 152016 Hom.: 40453 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.718 AC: 109282 AN: 152134 Hom.: 40474 Cov.: 33 AF XY: 0.709 AC XY: 52718 AN XY: 74366

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.750

Alfa AF: 0.796 Hom.: 58587

Bravo AF: 0.699

Asia WGS AF: 0.600 AC: 2092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	8.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2061333; hg19: chr19-44614208;