chr9-96778009-C-T

Variant names:

• chr9-96778009-C-T
• rs35334289
• ENST00000375231.5:c.-604G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000375231.5. 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.-177+25G>A		intron	N/A	NP_055745.1
	ZNF510	NM_001314059.2		c.-604G>A		5_prime_UTR	Exon 1 of 6	NP_001300988.1
	ZNF510	NM_001314060.2		c.-304+25G>A		intron	N/A	NP_001300989.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF510	ENST00000375231.5	TSL:1	c.-604G>A		5_prime_UTR	Exon 1 of 6	ENSP00000364379.1
	ZNF510	ENST00000223428.9	TSL:1 MANE Select	c.-177+25G>A		intron	N/A	ENSP00000223428.4
	ZNF510	ENST00000374641.3	TSL:2	n.96+25G>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 116

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.380 AC: 15767 AN: 41482

American (AMR) AF: 0.0663 AC: 1015 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1737 AN: 5158

South Asian (SAS) AF: 0.114 AC: 550 AN: 4826

European-Finnish (FIN) AF: 0.0928 AC: 984 AN: 10598

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

European-Non Finnish (NFE) AF: 0.0164 AC: 1115 AN: 68022

Other (OTH) AF: 0.0963 AC: 203 AN: 2108

Alfa AF: 0.0900 Hom.: 310

Bravo AF: 0.151

Asia WGS AF: 0.194 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.77
PhyloP100		-1.3
PromoterAI		-0.14	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs35334289; hg19: chr9-99540291;