rs3745770

Variant names:

• chr19-36997663-C-A
• rs3745770
• ENST00000591887.1:n.2141C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-36997663-C-A
• chr19-36997663-C-G
• chr19-36997663-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000591887.1(ZNF568):​n.2141C>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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF568 ENST00000591887.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 0 publications found

Genes affected

ZNF568 (HGNC:25392): (zinc finger protein 568) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in embryonic placenta morphogenesis and negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000291239 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF568	NM_001204838.2	c.*64C>A		3_prime_UTR_variant	Exon 10 of 10		NP_001191767.1
ZNF568	NM_001204839.2	c.*64C>A		3_prime_UTR_variant	Exon 9 of 9		NP_001191768.1
ZNF568	XM_017026772.2	c.*64C>A		3_prime_UTR_variant	Exon 10 of 10		XP_016882261.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291239	ENST00000706165.1	c.*64C>A		3_prime_UTR_variant	Exon 12 of 12			ENSP00000516244.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1080136 Hom.: 0 Cov.: 15 AF XY: 0.00 AC XY: 0 AN XY: 545756

African (AFR) AF: 0.00 AC: 0 AN: 24884

American (AMR) AF: 0.00 AC: 0 AN: 35306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23302

East Asian (EAS) AF: 0.00 AC: 0 AN: 34578

South Asian (SAS) AF: 0.00 AC: 0 AN: 72566

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35560

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5124

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 800962

Other (OTH) AF: 0.00 AC: 0 AN: 47854

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.7
DANN	Benign	0.70
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3745770; hg19: chr19-37488565;