rs4556941

Variant names:

• chr2-179762194-T-G
• rs4556941
• NM_152520.6:c.298+7309A>C

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+7309A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0498 in 152,180 control chromosomes in the GnomAD database, including 264 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 0.050 (264 hom., cov: 31)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152520.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	NM_152520.6	MANE Select	c.298+7309A>C		intron	N/A	NP_689733.4
	ZNF385B	NM_001352809.2		c.298+7309A>C		intron	N/A	NP_001339738.1
	ZNF385B	NM_001352810.2		c.298+7309A>C		intron	N/A	NP_001339739.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	ENST00000410066.7	TSL:1 MANE Select	c.298+7309A>C		intron	N/A	ENSP00000386845.2	A0A2U3TZT0

Frequencies

GnomAD3 genomes AF: 0.0498 AC: 7575 AN: 152060 Hom.: 264 Cov.: 31

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.0425

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.0388

Gnomad SAS AF: 0.0264

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0498 AC: 7572 AN: 152180 Hom.: 264 Cov.: 31 AF XY: 0.0501 AC XY: 3730 AN XY: 74408

African (AFR) AF: 0.0113 AC: 471 AN: 41536

American (AMR) AF: 0.0424 AC: 648 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3470

East Asian (EAS) AF: 0.0387 AC: 200 AN: 5166

South Asian (SAS) AF: 0.0264 AC: 127 AN: 4812

European-Finnish (FIN) AF: 0.0876 AC: 929 AN: 10606

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0664 AC: 4515 AN: 67988

Other (OTH) AF: 0.0507 AC: 107 AN: 2110

Alfa AF: 0.0601 Hom.: 145

Bravo AF: 0.0439

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.16
PhyloP100		-3.6
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: rs4556941; hg19: chr2-180626921;