rs7590028

Variant names:

• chr2-179684716-G-A
• rs7590028
• NM_152520.6:c.298+84787C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-179684716-G-A
• chr2-179684716-G-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+84787C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,926 control chromosomes in the GnomAD database, including 17,819 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 0.48 (17819 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.523 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.298+84787C>T		intron	N/A	NP_689733.4
	ZNF385B	NM_001352809.2		c.436+60997C>T		intron	N/A	NP_001339738.1
	ZNF385B	NM_001352810.2		c.298+84787C>T		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.298+84787C>T		intron	N/A	ENSP00000386845.2
	ZNF385B	ENST00000409343.5	TSL:2	c.25+60997C>T		intron	N/A	ENSP00000386379.1
	ZNF385B	ENST00000475539.5	TSL:4	n.142+60997C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73136 AN: 151808 Hom.: 17800 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.482 AC: 73199 AN: 151926 Hom.: 17819 Cov.: 32 AF XY: 0.482 AC XY: 35780 AN XY: 74232

African (AFR) AF: 0.484 AC: 20070 AN: 41434

American (AMR) AF: 0.533 AC: 8134 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1618 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1379 AN: 5166

South Asian (SAS) AF: 0.400 AC: 1925 AN: 4808

European-Finnish (FIN) AF: 0.523 AC: 5508 AN: 10536

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 33055 AN: 67934

Other (OTH) AF: 0.464 AC: 979 AN: 2112

Alfa AF: 0.480 Hom.: 55635

Bravo AF: 0.483

Asia WGS AF: 0.379 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.70
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: rs7590028; hg19: chr2-180549443;