rs2008230

chr2-179704259-A-Cchr2-179704259-A-Gchr2-179704259-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152520.6(ZNF385B):c.298+65244T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,088 control chromosomes in the GnomAD database, including 6,248 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 0.25 (6248 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6	c.298+65244T>G		intron_variant		ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7	c.298+65244T>G		intron_variant		1	NM_152520.6	P1
ZNF385B	ENST00000409343.5	c.25+41454T>G		intron_variant		2
ZNF385B	ENST00000475539.5	n.142+41454T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38407 AN: 151970 Hom.: 6228 Cov.: 32

Gnomad AFR AF: 0.0617

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.253 AC: 38443 AN: 152088 Hom.: 6248 Cov.: 32 AF XY: 0.264 AC XY: 19625 AN XY: 74332

Gnomad4 AFR AF: 0.0616

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.250

Alfa AF: 0.278 Hom.: 1479

Bravo AF: 0.247

Asia WGS AF: 0.458 AC: 1579 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.9
Dann	Benign	0.79

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: rs2008230; hg19: chr2-180568986;