chr2-179473465-C-A

Variant names:

• chr2-179473465-C-A
• rs9973399
• NM_152520.6:c.715+9807G>T

Variant summary

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

The NM_152520.6(ZNF385B):​c.715+9807G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,086 control chromosomes in the GnomAD database, including 1,471 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 0.12 (1471 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.715+9807G>T		intron_variant	Intron 6 of 9	ENST00000410066.7	NP_689733.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385B	ENST00000410066.7	c.715+9807G>T		intron_variant	Intron 6 of 9	1	NM_152520.6	ENSP00000386845.2

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18296 AN: 151968 Hom.: 1468 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00926

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.120 AC: 18320 AN: 152086 Hom.: 1471 Cov.: 32 AF XY: 0.122 AC XY: 9036 AN XY: 74356

African (AFR) AF: 0.216 AC: 8953 AN: 41454

American (AMR) AF: 0.0922 AC: 1409 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3470

East Asian (EAS) AF: 0.00948 AC: 49 AN: 5170

South Asian (SAS) AF: 0.168 AC: 809 AN: 4818

European-Finnish (FIN) AF: 0.0701 AC: 742 AN: 10582

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0810 AC: 5507 AN: 67998

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.106 Hom.: 282

Bravo AF: 0.124

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.49
PhyloP100		-0.74
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: rs9973399; hg19: chr2-180338192;