rs13009601

Variant names:

• chr2-179638094-A-G
• rs13009601
• NM_152520.6:c.299-93125T>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.299-93125T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,136 control chromosomes in the GnomAD database, including 2,429 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 0.17 (2429 hom., cov: 33)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.299-93125T>C		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.299-93125T>C		intron_variant	Intron 3 of 9	1	NM_152520.6	ENSP00000386845.2
ZNF385B	ENST00000409343.5	c.26-93125T>C		intron_variant	Intron 1 of 7	2		ENSP00000386379.1
ZNF385B	ENST00000463918.1	n.106+21983T>C		intron_variant	Intron 1 of 1	3
ZNF385B	ENST00000475539.5	n.142+107619T>C		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26489 AN: 152018 Hom.: 2415 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.174 AC: 26539 AN: 152136 Hom.: 2429 Cov.: 33 AF XY: 0.176 AC XY: 13126 AN XY: 74382

African (AFR) AF: 0.205 AC: 8489 AN: 41502

American (AMR) AF: 0.240 AC: 3664 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 640 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1060 AN: 5172

South Asian (SAS) AF: 0.159 AC: 766 AN: 4822

European-Finnish (FIN) AF: 0.146 AC: 1543 AN: 10588

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9870 AN: 68000

Other (OTH) AF: 0.178 AC: 376 AN: 2112

Alfa AF: 0.155 Hom.: 936

Bravo AF: 0.185

Asia WGS AF: 0.228 AC: 789 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		0.33
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: rs13009601; hg19: chr2-180502821;