rs2008230

Variant names:

• chr2-179704259-A-C
• rs2008230
• NM_152520.6:c.298+65244T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-179704259-A-C
• chr2-179704259-A-G
• chr2-179704259-A-T

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+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
• 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=-0.88).
• 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 rank	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.298+65244T>G		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.298+65244T>G		intron_variant	Intron 3 of 9	1	NM_152520.6	ENSP00000386845.2
ZNF385B	ENST00000409343.5	c.25+41454T>G		intron_variant	Intron 1 of 7	2		ENSP00000386379.1
ZNF385B	ENST00000475539.5	n.142+41454T>G		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.0616 AC: 2559 AN: 41536

American (AMR) AF: 0.383 AC: 5851 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1015 AN: 3472

East Asian (EAS) AF: 0.556 AC: 2862 AN: 5152

South Asian (SAS) AF: 0.418 AC: 2015 AN: 4816

European-Finnish (FIN) AF: 0.340 AC: 3581 AN: 10546

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19763 AN: 67964

Other (OTH) AF: 0.250 AC: 527 AN: 2110

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
PhyloP100		-0.28
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: rs2008230; hg19: chr2-180568986;