rs12693204

Variant names:

• chr2-179689561-T-C
• rs12693204
• NM_152520.6:c.298+79942A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152520.6(ZNF385B):​c.298+79942A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,894 control chromosomes in the GnomAD database, including 15,422 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 0.45 (15422 hom., cov: 31)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.298+79942A>G		intron_variant	Intron 3 of 9	ENST00000410066.7	NP_689733.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385B	ENST00000410066.7	c.298+79942A>G		intron_variant	Intron 3 of 9	1	NM_152520.6	ENSP00000386845.2
ZNF385B	ENST00000409343.5	c.25+56152A>G		intron_variant	Intron 1 of 7	2		ENSP00000386379.1
ZNF385B	ENST00000475539.5	n.142+56152A>G		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67919 AN: 151776 Hom.: 15415 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.447 AC: 67954 AN: 151894 Hom.: 15422 Cov.: 31 AF XY: 0.444 AC XY: 32975 AN XY: 74266

African (AFR) AF: 0.496 AC: 20529 AN: 41408

American (AMR) AF: 0.449 AC: 6853 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1443 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1103 AN: 5148

South Asian (SAS) AF: 0.338 AC: 1627 AN: 4810

European-Finnish (FIN) AF: 0.424 AC: 4481 AN: 10562

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30471 AN: 67914

Other (OTH) AF: 0.429 AC: 905 AN: 2112

Alfa AF: 0.457 Hom.: 14581

Bravo AF: 0.455

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.56
DANN	Benign	0.64
PhyloP100		-0.063
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12693204; hg19: chr2-180554288;