rs6708300

chr2-179487999-A-G

Variant summary

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

The NM_152520.6(ZNF385B):c.553-4565T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,134 control chromosomes in the GnomAD database, including 5,586 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 0.27 (5586 hom., cov: 33)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6	c.553-4565T>C		intron_variant		ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7	c.553-4565T>C		intron_variant		1	NM_152520.6	P1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40555 AN: 152016 Hom.: 5583 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.267 AC: 40581 AN: 152134 Hom.: 5586 Cov.: 33 AF XY: 0.268 AC XY: 19927 AN XY: 74348

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.258

Alfa AF: 0.266 Hom.: 923

Bravo AF: 0.260

Asia WGS AF: 0.378 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.59
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6708300; hg19: chr2-180352726;