2-179503335-T-C

Position:

• chr2-179503335-T-C

Variant summary

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

The NM_152520.6(ZNF385B):​c.552+15193A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,178 control chromosomes in the GnomAD database, including 53,021 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 0.83 (53021 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6	c.552+15193A>G		intron_variant		ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7	c.552+15193A>G		intron_variant		1	NM_152520.6	P1

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126585 AN: 152060 Hom.: 52989 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.832 AC: 126669 AN: 152178 Hom.: 53021 Cov.: 32 AF XY: 0.835 AC XY: 62112 AN XY: 74394

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.829

Alfa AF: 0.845 Hom.: 10375

Bravo AF: 0.828

Asia WGS AF: 0.911 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.54

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: rs10183243; hg19: chr2-180368062;