rs17770666

Variant names:

• chr2-179666762-T-C
• rs17770666
• NM_152520.6:c.298+102741A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-179666762-T-C
• chr2-179666762-T-G

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+102741A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,192 control chromosomes in the GnomAD database, including 2,024 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 0.16 (2024 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.298+102741A>G		intron_variant	Intron 3 of 9	ENST00000410066.7	NP_689733.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385B	ENST00000410066.7	c.298+102741A>G		intron_variant	Intron 3 of 9	1	NM_152520.6	ENSP00000386845.2
ZNF385B	ENST00000409343.5	c.25+78951A>G		intron_variant	Intron 1 of 7	2		ENSP00000386379.1
ZNF385B	ENST00000475539.5	n.142+78951A>G		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24506 AN: 152074 Hom.: 2019 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.161 AC: 24529 AN: 152192 Hom.: 2024 Cov.: 32 AF XY: 0.164 AC XY: 12189 AN XY: 74416

African (AFR) AF: 0.152 AC: 6295 AN: 41518

American (AMR) AF: 0.187 AC: 2858 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3468

East Asian (EAS) AF: 0.0330 AC: 171 AN: 5188

South Asian (SAS) AF: 0.190 AC: 916 AN: 4822

European-Finnish (FIN) AF: 0.209 AC: 2210 AN: 10580

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11137 AN: 67998

Other (OTH) AF: 0.151 AC: 319 AN: 2114

Alfa AF: 0.101 Hom.: 186

Bravo AF: 0.158

Asia WGS AF: 0.123 AC: 426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.57
PhyloP100		-0.26
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: rs17770666; hg19: chr2-180531489;