rs12761705

Variant names:

• chr10-96161042-C-A
• rs12761705
• ENST00000534948.2:n.5551C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-96161042-C-A
• chr10-96161042-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000534948.2(ZNF518A):​n.5551C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF518A ENST00000534948.2 non_coding_transcript_exon
• 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF518A	NM_001330736.2	c.*268C>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000316045.10	NP_001317665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF518A	ENST00000316045.10	c.*268C>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_001330736.2	ENSP00000479684.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 162002 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 82086

African (AFR) AF: 0.00 AC: 0 AN: 4668

American (AMR) AF: 0.00 AC: 0 AN: 5088

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5612

East Asian (EAS) AF: 0.00 AC: 0 AN: 11552

South Asian (SAS) AF: 0.00 AC: 0 AN: 2878

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22790

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 756

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 98708

Other (OTH) AF: 0.00 AC: 0 AN: 9950

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 2289

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	11
DANN	Benign	0.81
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;