chr2-179503335-T-C

Variant names:

• chr2-179503335-T-C
• rs10183243
• NM_152520.6:c.552+15193A>G

Variant summary

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

The NM_152520.6(ZNF385B):​c.552+15193A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,178 control chromosomes in the GnomAD database, including 53,021 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 0.83 (53021 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 2 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	NM_152520.6	MANE Select	c.552+15193A>G		intron	N/A	NP_689733.4
	ZNF385B	NM_001352809.2		c.690+15193A>G		intron	N/A	NP_001339738.1
	ZNF385B	NM_001352810.2		c.552+15193A>G		intron	N/A	NP_001339739.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	ENST00000410066.7	TSL:1 MANE Select	c.552+15193A>G		intron	N/A	ENSP00000386845.2
	ZNF385B	ENST00000466398.5	TSL:1	n.781+10750A>G		intron	N/A
	ZNF385B	ENST00000409343.5	TSL:2	c.279+15193A>G		intron	N/A	ENSP00000386379.1

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126585 AN: 152060 Hom.: 52989 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.832 AC: 126669 AN: 152178 Hom.: 53021 Cov.: 32 AF XY: 0.835 AC XY: 62112 AN XY: 74394

African (AFR) AF: 0.748 AC: 31011 AN: 41484

American (AMR) AF: 0.866 AC: 13234 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2883 AN: 3472

East Asian (EAS) AF: 0.924 AC: 4784 AN: 5180

South Asian (SAS) AF: 0.923 AC: 4449 AN: 4822

European-Finnish (FIN) AF: 0.860 AC: 9109 AN: 10586

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58489 AN: 68028

Other (OTH) AF: 0.829 AC: 1751 AN: 2112

Alfa AF: 0.842 Hom.: 10579

Bravo AF: 0.828

Asia WGS AF: 0.911 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.54
PhyloP100		-0.14
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: rs10183243; hg19: chr2-180368062;