chr2-179732769-C-T

Variant names:

• chr2-179732769-C-T
• rs2126424
• NM_152520.6:c.298+36734G>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+36734G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0915 in 152,168 control chromosomes in the GnomAD database, including 716 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 0.091 (716 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	NM_152520.6	MANE Select	c.298+36734G>A		intron	N/A	NP_689733.4
	ZNF385B	NM_001352809.2		c.436+12944G>A		intron	N/A	NP_001339738.1
	ZNF385B	NM_001352810.2		c.298+36734G>A		intron	N/A	NP_001339739.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	ENST00000410066.7	TSL:1 MANE Select	c.298+36734G>A		intron	N/A	ENSP00000386845.2
	ZNF385B	ENST00000409343.5	TSL:2	c.25+12944G>A		intron	N/A	ENSP00000386379.1
	ZNF385B	ENST00000475539.5	TSL:4	n.142+12944G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0915 AC: 13908 AN: 152050 Hom.: 714 Cov.: 32

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0630

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.0711

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0997

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

GnomAD4 genome AF: 0.0915 AC: 13917 AN: 152168 Hom.: 716 Cov.: 32 AF XY: 0.0866 AC XY: 6440 AN XY: 74390

African (AFR) AF: 0.0882 AC: 3661 AN: 41520

American (AMR) AF: 0.0630 AC: 963 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0462 AC: 160 AN: 3462

East Asian (EAS) AF: 0.00579 AC: 30 AN: 5182

South Asian (SAS) AF: 0.0760 AC: 366 AN: 4818

European-Finnish (FIN) AF: 0.0711 AC: 753 AN: 10590

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7739 AN: 67986

Other (OTH) AF: 0.0991 AC: 209 AN: 2108

Alfa AF: 0.0953 Hom.: 83

Bravo AF: 0.0905

Asia WGS AF: 0.0530 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.66
PhyloP100		0.014
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: rs2126424; hg19: chr2-180597496;