rs17824619

Positions:

• chr2-179744116-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+25387T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,146 control chromosomes in the GnomAD database, including 1,099 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 0.10 (1099 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79

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=-0.54).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.298+25387T>A		intron_variant		ENST00000410066.7	NP_689733.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF385B	ENST00000410066.7	c.298+25387T>A		intron_variant		1	NM_152520.6	ENSP00000386845	P1
ZNF385B	ENST00000409343.5	c.25+1597T>A		intron_variant		2		ENSP00000386379
ZNF385B	ENST00000475539.5	n.142+1597T>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15838 AN: 152030 Hom.: 1094 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0830

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.104 AC: 15840 AN: 152146 Hom.: 1099 Cov.: 32 AF XY: 0.104 AC XY: 7706 AN XY: 74360

Gnomad4 AFR AF: 0.0275

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0830

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.116

Alfa AF: 0.118 Hom.: 171

Bravo AF: 0.109

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	10
DANN	Benign	0.76

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: rs17824619; hg19: chr2-180608843;