rs10816533

Variant names:

• chr9-96776856-G-C
• rs10816533
• NM_014930.3:c.-176-611C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014930.3(ZNF510):​c.-176-611C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,062 control chromosomes in the GnomAD database, including 4,070 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 0.15 (4070 hom., cov: 32)
• Consequence: ZNF510 NM_014930.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 17 publications found

Genes affected

ZNF510 (HGNC:29161): (zinc finger protein 510) This gene encodes a krueppel C2H2-type zinc-finger protein family member. The encoded protein is expressed in several cancer cell types and may be a biomarker for early diagnosis of these cancers. [provided by RefSeq, Sep 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014930.3. 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
	ZNF510	NM_014930.3	MANE Select	c.-176-611C>G		intron	N/A	NP_055745.1
	ZNF510	NM_001314059.2		c.-176-611C>G		intron	N/A	NP_001300988.1
	ZNF510	NM_001314060.2		c.-303-611C>G		intron	N/A	NP_001300989.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF510	ENST00000223428.9	TSL:1 MANE Select	c.-176-611C>G		intron	N/A	ENSP00000223428.4
	ZNF510	ENST00000375231.5	TSL:1	c.-176-611C>G		intron	N/A	ENSP00000364379.1
	ZNF510	ENST00000374641.3	TSL:2	n.97-611C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22936 AN: 151944 Hom.: 4035 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.151 AC: 23012 AN: 152062 Hom.: 4070 Cov.: 32 AF XY: 0.154 AC XY: 11480 AN XY: 74326

African (AFR) AF: 0.416 AC: 17231 AN: 41454

American (AMR) AF: 0.0694 AC: 1061 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1738 AN: 5146

South Asian (SAS) AF: 0.115 AC: 551 AN: 4812

European-Finnish (FIN) AF: 0.0932 AC: 987 AN: 10586

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0164 AC: 1116 AN: 68002

Other (OTH) AF: 0.100 AC: 211 AN: 2106

Alfa AF: 0.0510 Hom.: 598

Bravo AF: 0.162

Asia WGS AF: 0.197 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.71
PhyloP100		-0.016
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: rs10816533; hg19: chr9-99539138;