10-96161042-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001330736.2(ZNF518A):c.*268C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 313,274 control chromosomes in the GnomAD database, including 28,061 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 0.37 (11916 hom., cov: 32)
  • Exomes 𝑓: 0.43 (16145 hom.)
• Consequence: ZNF518A NM_001330736.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

Genes affected

ZNF518A (HGNC:29009): (zinc finger protein 518A) The protein encoded by this gene is a member of the krueppel C2H2-type zinc finger protein family. The encoded protein contains five zinc fingers and is likely a nuclear transcriptional regulator. Numerous transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF518A	NM_001330736.2	c.*268C>T		3_prime_UTR_variant	6/6	ENST00000316045.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF518A	ENST00000316045.10	c.*268C>T		3_prime_UTR_variant	6/6	1	NM_001330736.2	P1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56715 AN: 151720 Hom.: 11919 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.399

GnomAD4 exome AF: 0.429 AC: 69276 AN: 161436 Hom.: 16145 Cov.: 4 AF XY: 0.431 AC XY: 35277 AN XY: 81790

Gnomad4 AFR exome AF: 0.220

Gnomad4 AMR exome AF: 0.404

Gnomad4 ASJ exome AF: 0.538

Gnomad4 EAS exome AF: 0.0184

Gnomad4 SAS exome AF: 0.289

Gnomad4 FIN exome AF: 0.434

Gnomad4 NFE exome AF: 0.486

Gnomad4 OTH exome AF: 0.423

GnomAD4 genome AF: 0.374 AC: 56733 AN: 151838 Hom.: 11916 Cov.: 32 AF XY: 0.368 AC XY: 27290 AN XY: 74220

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.0266

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.395

Alfa AF: 0.399 Hom.: 2270

Bravo AF: 0.367

Asia WGS AF: 0.140 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	11
Dann	Benign	0.84

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: rs12761705; hg19: chr10-97920798;