chr10-96161042-C-T

Variant names:

• chr10-96161042-C-T
• rs12761705
• NM_001330736.2:c.*268C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330736.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF518A	NM_001330736.2	MANE Select	c.*268C>T		3_prime_UTR	Exon 6 of 6	NP_001317665.1	Q6AHZ1-1
	ZNF518A	NM_001278524.2		c.*268C>T		3_prime_UTR	Exon 7 of 7	NP_001265453.1	Q6AHZ1-1
	ZNF518A	NM_001278525.2		c.*268C>T		3_prime_UTR	Exon 6 of 6	NP_001265454.1	Q6AHZ1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF518A	ENST00000316045.10	TSL:1 MANE Select	c.*268C>T		3_prime_UTR	Exon 6 of 6	ENSP00000479684.1	Q6AHZ1-1
	ZNF518A	ENST00000624776.4	TSL:1	c.*268C>T		3_prime_UTR	Exon 6 of 6	ENSP00000485614.1	Q6AHZ1-1
	ZNF518A	ENST00000534948.2	TSL:1	n.5551C>T		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.220 AC: 1025 AN: 4658

American (AMR) AF: 0.404 AC: 2043 AN: 5062

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 3003 AN: 5580

East Asian (EAS) AF: 0.0184 AC: 212 AN: 11546

South Asian (SAS) AF: 0.289 AC: 830 AN: 2872

European-Finnish (FIN) AF: 0.434 AC: 9872 AN: 22750

Middle Eastern (MID) AF: 0.468 AC: 353 AN: 754

European-Non Finnish (NFE) AF: 0.486 AC: 47753 AN: 98314

Other (OTH) AF: 0.423 AC: 4185 AN: 9900

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

African (AFR) AF: 0.211 AC: 8755 AN: 41430

American (AMR) AF: 0.407 AC: 6200 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1812 AN: 3454

East Asian (EAS) AF: 0.0266 AC: 138 AN: 5182

South Asian (SAS) AF: 0.300 AC: 1449 AN: 4822

European-Finnish (FIN) AF: 0.426 AC: 4489 AN: 10540

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32450 AN: 67854

Other (OTH) AF: 0.395 AC: 832 AN: 2106

Alfa AF: 0.394 Hom.: 2289

Bravo AF: 0.367

Asia WGS AF: 0.140 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		0.43

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: rs12761705; hg19: chr10-97920798;