rs16866933

chr2-179701951-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.298+67552C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0983 in 152,194 control chromosomes in the GnomAD database, including 1,165 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 0.098 (1165 hom., cov: 33)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6	c.298+67552C>T		intron_variant		ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7	c.298+67552C>T		intron_variant		1	NM_152520.6	P1
ZNF385B	ENST00000409343.5	c.25+43762C>T		intron_variant		2
ZNF385B	ENST00000475539.5	n.142+43762C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0981 AC: 14926 AN: 152076 Hom.: 1152 Cov.: 33

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0772

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0983 AC: 14962 AN: 152194 Hom.: 1165 Cov.: 33 AF XY: 0.106 AC XY: 7858 AN XY: 74398

Gnomad4 AFR AF: 0.0592

Gnomad4 AMR AF: 0.0770

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.0834

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.0934 Hom.: 1956

Bravo AF: 0.0882

Asia WGS AF: 0.293 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.9
Dann	Benign	0.79

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: rs16866933; hg19: chr2-180566678;