rs1139

Variant names:

• chr2-179745354-C-T
• rs1139
• NM_152520.6:c.298+24149G>A

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+24149G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,044 control chromosomes in the GnomAD database, including 4,327 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 0.23 (4327 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 7 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	NM_152520.6	MANE Select	c.298+24149G>A		intron	N/A	NP_689733.4
	ZNF385B	NM_001352809.2		c.436+359G>A		intron	N/A	NP_001339738.1
	ZNF385B	NM_001352810.2		c.298+24149G>A		intron	N/A	NP_001339739.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	ENST00000410066.7	TSL:1 MANE Select	c.298+24149G>A		intron	N/A	ENSP00000386845.2	A0A2U3TZT0
	ZNF385B	ENST00000409343.5	TSL:2	c.25+359G>A		intron	N/A	ENSP00000386379.1	Q569K4-2
	ZNF385B	ENST00000475539.5	TSL:4	n.142+359G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34414 AN: 151926 Hom.: 4316 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.227 AC: 34443 AN: 152044 Hom.: 4327 Cov.: 32 AF XY: 0.231 AC XY: 17189 AN XY: 74298

African (AFR) AF: 0.195 AC: 8115 AN: 41510

American (AMR) AF: 0.150 AC: 2283 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3468

East Asian (EAS) AF: 0.488 AC: 2519 AN: 5158

South Asian (SAS) AF: 0.279 AC: 1344 AN: 4822

European-Finnish (FIN) AF: 0.305 AC: 3217 AN: 10562

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15774 AN: 67944

Other (OTH) AF: 0.219 AC: 462 AN: 2110

Alfa AF: 0.228 Hom.: 509

Bravo AF: 0.214

Asia WGS AF: 0.357 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.022
DANN	Benign	0.24
PhyloP100		-0.82
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: rs1139; hg19: chr2-180610081;