rs79525531

Variant names:

• chr19-11580994-G-A
• rs79525531
• ENST00000585493.5:c.-94+5641G>A

Variant summary

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

The ENST00000585493.5(ZNF627):​c.-94+5641G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0947 in 152,122 control chromosomes in the GnomAD database, including 853 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 0.095 (853 hom., cov: 30)
• Consequence: ZNF627 ENST00000585493.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607
• Publications: 5 publications found

Genes affected

ZNF627 (HGNC:30570): (zinc finger protein 627) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

LOC124904638 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585493.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF627	ENST00000585493.5	TSL:4	c.-94+5641G>A		intron	N/A	ENSP00000464997.1	K7EJ27
	ZNF627	ENST00000593279.5	TSL:4	n.519+5641G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14402 AN: 152004 Hom.: 852 Cov.: 30

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.0947 AC: 14401 AN: 152122 Hom.: 853 Cov.: 30 AF XY: 0.0946 AC XY: 7030 AN XY: 74348

African (AFR) AF: 0.0311 AC: 1292 AN: 41526

American (AMR) AF: 0.0818 AC: 1248 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3468

East Asian (EAS) AF: 0.0832 AC: 431 AN: 5182

South Asian (SAS) AF: 0.0900 AC: 434 AN: 4820

European-Finnish (FIN) AF: 0.158 AC: 1674 AN: 10572

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8449 AN: 67986

Other (OTH) AF: 0.117 AC: 248 AN: 2112

Alfa AF: 0.108 Hom.: 124

Bravo AF: 0.0875

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.51
PhyloP100		0.61

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs79525531;

hg19: chr19-11691809;