NM_152520.6:c.299-45371C>T

Variant names:

• chr2-179590340-G-A
• rs13411180
• NM_152520.6:c.299-45371C>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.299-45371C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,120 control chromosomes in the GnomAD database, including 2,930 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 0.19 (2930 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.299-45371C>T		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.299-45371C>T		intron_variant	Intron 3 of 9	1	NM_152520.6	ENSP00000386845.2

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28433 AN: 152000 Hom.: 2926 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.187 AC: 28471 AN: 152120 Hom.: 2930 Cov.: 32 AF XY: 0.188 AC XY: 14000 AN XY: 74364

African (AFR) AF: 0.242 AC: 10048 AN: 41488

American (AMR) AF: 0.261 AC: 3990 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1230 AN: 5178

South Asian (SAS) AF: 0.161 AC: 773 AN: 4816

European-Finnish (FIN) AF: 0.169 AC: 1788 AN: 10592

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9369 AN: 67970

Other (OTH) AF: 0.192 AC: 406 AN: 2116

Alfa AF: 0.157 Hom.: 8638

Bravo AF: 0.196

Asia WGS AF: 0.206 AC: 714 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	3.2
DANN	Benign	0.78
PhyloP100		0.23
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: rs13411180; hg19: chr2-180455067;