rs1549492

Variant names:

• chr19-58073880-A-G
• rs1549492
• ENST00000515535.1:n.161-7813A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000515535.1(ZNF135):​n.161-7813A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 151,970 control chromosomes in the GnomAD database, including 36,574 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 0.69 (36574 hom., cov: 31)
• Consequence: ZNF135 ENST00000515535.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 2 publications found

Genes affected

ZNF135 (HGNC:12919): (zinc finger protein 135) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in cytoskeleton organization and regulation of cell morphogenesis. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF135	ENST00000515535.1	n.161-7813A>G		intron_variant	Intron 2 of 3	2		ENSP00000471344.1

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104976 AN: 151852 Hom.: 36541 Cov.: 31

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.693

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.691 AC: 105060 AN: 151970 Hom.: 36574 Cov.: 31 AF XY: 0.688 AC XY: 51064 AN XY: 74258

African (AFR) AF: 0.761 AC: 31526 AN: 41446

American (AMR) AF: 0.675 AC: 10296 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2421 AN: 3472

East Asian (EAS) AF: 0.496 AC: 2550 AN: 5144

South Asian (SAS) AF: 0.666 AC: 3208 AN: 4820

European-Finnish (FIN) AF: 0.702 AC: 7407 AN: 10554

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45381 AN: 67956

Other (OTH) AF: 0.687 AC: 1451 AN: 2112

Alfa AF: 0.679 Hom.: 4393

Bravo AF: 0.695

Asia WGS AF: 0.545 AC: 1900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.1
DANN	Benign	0.71
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1549492; hg19: chr19-58585248;