rs6757845

Positions:

• chr2-179449268-T-C
• chr2-179449268-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152520.6(ZNF385B):​c.716-2498A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,850 control chromosomes in the GnomAD database, including 33,878 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 0.66 (33878 hom., cov: 31)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541

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]

ZNF385B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.716-2498A>G		intron_variant		ENST00000410066.7	NP_689733.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF385B	ENST00000410066.7	c.716-2498A>G		intron_variant		1	NM_152520.6	ENSP00000386845.2

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100147 AN: 151732 Hom.: 33824 Cov.: 31

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.660 AC: 100262 AN: 151850 Hom.: 33878 Cov.: 31 AF XY: 0.665 AC XY: 49339 AN XY: 74214

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.653

Alfa AF: 0.595 Hom.: 53710

Bravo AF: 0.661

Asia WGS AF: 0.855 AC: 2973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	9.7
DANN	Benign	0.47

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: rs6757845; hg19: chr2-180313995;