2-179474929-C-A

Variant names:

• chr2-179474929-C-A
• rs6744352
• NM_152520.6:c.715+8343G>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+8343G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,072 control chromosomes in the GnomAD database, including 2,093 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 0.16 (2093 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.715+8343G>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+8343G>T		intron_variant	Intron 6 of 9	1	NM_152520.6	ENSP00000386845.2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23795 AN: 151954 Hom.: 2093 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0174

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.157 AC: 23805 AN: 152072 Hom.: 2093 Cov.: 32 AF XY: 0.155 AC XY: 11512 AN XY: 74314

African (AFR) AF: 0.106 AC: 4406 AN: 41470

American (AMR) AF: 0.145 AC: 2212 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3470

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5174

South Asian (SAS) AF: 0.206 AC: 991 AN: 4818

European-Finnish (FIN) AF: 0.175 AC: 1848 AN: 10554

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13158 AN: 67976

Other (OTH) AF: 0.186 AC: 393 AN: 2116

Alfa AF: 0.153 Hom.: 796

Bravo AF: 0.149

Asia WGS AF: 0.122 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		-0.66
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: rs6744352; hg19: chr2-180339656;