rs1161648

chr2-179756119-C-Achr2-179756119-C-Tchr2-179756119-C-G

Variant summary

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

The NM_152520.6(ZNF385B):c.298+13384G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 151,800 control chromosomes in the GnomAD database, including 53,431 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 0.84 (53431 hom., cov: 28)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6	c.298+13384G>T		intron_variant		ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7	c.298+13384G>T		intron_variant		1	NM_152520.6	P1

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127125 AN: 151682 Hom.: 53392 Cov.: 28

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.838 AC: 127217 AN: 151800 Hom.: 53431 Cov.: 28 AF XY: 0.843 AC XY: 62527 AN XY: 74182

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.820

Gnomad4 OTH AF: 0.833

Alfa AF: 0.776 Hom.: 2214

Bravo AF: 0.842

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.035
Dann	Benign	0.40

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: rs356416; hg19: chr2-180620846;