rs35334289

Positions:

• chr9-96778009-C-T

Variant summary

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

The ENST00000375231.5(ZNF510):​c.-604G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,172 control chromosomes in the GnomAD database, including 3,457 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 0.14 (3457 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF510 ENST00000375231.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF510	NM_014930.3	c.-177+25G>A		intron_variant		ENST00000223428.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF510	ENST00000375231.5	c.-604G>A		5_prime_UTR_variant	1/6	1		P1
ZNF510	ENST00000223428.9	c.-177+25G>A		intron_variant		1	NM_014930.3	P1
ZNF510	ENST00000374641.3	n.96+25G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21416 AN: 152056 Hom.: 3423 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0665

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0973

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 142 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 104

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.141 AC: 21488 AN: 152172 Hom.: 3457 Cov.: 32 AF XY: 0.145 AC XY: 10779 AN XY: 74376

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.0663

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0928

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0963

Alfa AF: 0.0794 Hom.: 256

Bravo AF: 0.151

Asia WGS AF: 0.194 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs35334289; hg19: chr9-99540291;