rs9288039

chr2-179512573-G-A

Variant summary

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

The NM_152520.6(ZNF385B):c.552+5955C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,074 control chromosomes in the GnomAD database, including 40,389 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 (40389 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524

Genes affected

ZNF385B (HGNC:26332): (zinc finger protein 385B) Enables p53 binding activity. Involved in intrinsic apoptotic signaling pathway by p53 class mediator. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6	c.552+5955C>T		intron_variant		ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7	c.552+5955C>T		intron_variant		1	NM_152520.6	P1

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109552 AN: 151956 Hom.: 40365 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.721 AC: 109612 AN: 152074 Hom.: 40389 Cov.: 32 AF XY: 0.726 AC XY: 53944 AN XY: 74334

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.693

Alfa AF: 0.752 Hom.: 22406

Bravo AF: 0.713

Asia WGS AF: 0.809 AC: 2813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.60
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9288039; hg19: chr2-180377300;