rs7590028

chr2-179684716-G-Achr2-179684716-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6	c.298+84787C>T		intron_variant		ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7	c.298+84787C>T		intron_variant		1	NM_152520.6	P1
ZNF385B	ENST00000409343.5	c.25+60997C>T		intron_variant		2
ZNF385B	ENST00000475539.5	n.142+60997C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.464

Alfa AF: 0.477 Hom.: 34567

Bravo AF: 0.483

Asia WGS AF: 0.379 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.1
Dann	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs7590028; hg19: chr2-180549443;