chr2-179501964-T-A

Variant names:

• chr2-179501964-T-A
• rs1517702
• NM_152520.6:c.552+16564A>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.552+16564A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,056 control chromosomes in the GnomAD database, including 16,814 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 0.44 (16814 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 0 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=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.552+16564A>T		intron_variant	Intron 5 of 9	ENST00000410066.7	NP_689733.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385B	ENST00000410066.7	c.552+16564A>T		intron_variant	Intron 5 of 9	1	NM_152520.6	ENSP00000386845.2

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67030 AN: 151938 Hom.: 16818 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.441 AC: 67039 AN: 152056 Hom.: 16814 Cov.: 32 AF XY: 0.436 AC XY: 32384 AN XY: 74312

African (AFR) AF: 0.261 AC: 10830 AN: 41492

American (AMR) AF: 0.365 AC: 5565 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1724 AN: 3464

East Asian (EAS) AF: 0.0210 AC: 109 AN: 5180

South Asian (SAS) AF: 0.414 AC: 2000 AN: 4828

European-Finnish (FIN) AF: 0.581 AC: 6131 AN: 10560

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39062 AN: 67962

Other (OTH) AF: 0.452 AC: 953 AN: 2108

Alfa AF: 0.512 Hom.: 2651

Bravo AF: 0.411

Asia WGS AF: 0.221 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.1
DANN	Benign	0.85
PhyloP100		0.21
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: rs1517702; hg19: chr2-180366691;