chr2-179703346-C-T

Position:

• chr2-179703346-C-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+66157G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,098 control chromosomes in the GnomAD database, including 9,013 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 0.33 (9013 hom., cov: 33)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6	c.298+66157G>A		intron_variant		ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7	c.298+66157G>A		intron_variant		1	NM_152520.6	P1
ZNF385B	ENST00000409343.5	c.25+42367G>A		intron_variant		2
ZNF385B	ENST00000475539.5	n.142+42367G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49604 AN: 151978 Hom.: 8996 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.326 AC: 49638 AN: 152098 Hom.: 9013 Cov.: 33 AF XY: 0.328 AC XY: 24397 AN XY: 74386

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.327

Alfa AF: 0.367 Hom.: 9973

Bravo AF: 0.309

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.70

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: rs11885327; hg19: chr2-180568073;