rs356416

Variant names:

• chr2-179756119-C-A
• rs356416
• NM_152520.6:c.298+13384G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-179756119-C-A
• chr2-179756119-C-G
• chr2-179756119-C-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.298+13384G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 151,800 control chromosomes in the GnomAD database, including 53,431 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 0.84 (53431 hom., cov: 28)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.965 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+13384G>T		intron	N/A	NP_689733.4
	ZNF385B	NM_001352809.2		c.299-10269G>T		intron	N/A	NP_001339738.1
	ZNF385B	NM_001352810.2		c.298+13384G>T		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+13384G>T		intron	N/A	ENSP00000386845.2	A0A2U3TZT0

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127125 AN: 151682 Hom.: 53392 Cov.: 28

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.838 AC: 127217 AN: 151800 Hom.: 53431 Cov.: 28 AF XY: 0.843 AC XY: 62527 AN XY: 74182

African (AFR) AF: 0.824 AC: 34079 AN: 41344

American (AMR) AF: 0.886 AC: 13519 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3028 AN: 3466

East Asian (EAS) AF: 0.987 AC: 5088 AN: 5154

South Asian (SAS) AF: 0.899 AC: 4297 AN: 4778

European-Finnish (FIN) AF: 0.842 AC: 8892 AN: 10558

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.820 AC: 55723 AN: 67942

Other (OTH) AF: 0.833 AC: 1750 AN: 2102

Alfa AF: 0.776 Hom.: 2214

Bravo AF: 0.842

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.035
DANN	Benign	0.40
PhyloP100		-3.4
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: rs356416; hg19: chr2-180620846;