rs9973399

chr2-179473465-C-A

Variant summary

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

The NM_152520.6(ZNF385B):c.715+9807G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,086 control chromosomes in the GnomAD database, including 1,471 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 0.12 (1471 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6	c.715+9807G>T		intron_variant		ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7	c.715+9807G>T		intron_variant		1	NM_152520.6	P1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18296 AN: 151968 Hom.: 1468 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00926

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.120 AC: 18320 AN: 152086 Hom.: 1471 Cov.: 32 AF XY: 0.122 AC XY: 9036 AN XY: 74356

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.0922

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00948

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0701

Gnomad4 NFE AF: 0.0810

Gnomad4 OTH AF: 0.144

Alfa AF: 0.106 Hom.: 282

Bravo AF: 0.124

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.28
Dann	Benign	0.49

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: rs9973399; hg19: chr2-180338192;