19-37131109-T-C

Variant names:

• chr19-37131109-T-C
• rs4805201
• ENST00000588873.1:c.253+24756A>G

Variant summary

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

The ENST00000588873.1(ENSG00000267360):​c.253+24756A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,626 control chromosomes in the GnomAD database, including 17,116 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 0.47 (17116 hom., cov: 31)
• Consequence: ENSG00000267360 ENST00000588873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914
• Publications: 4 publications found

Genes affected

ENSG00000267360 (HGNC:):

ZNF585A (HGNC:26305): (zinc finger protein 585A) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000588873.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267360	ENST00000588873.1	TSL:5	c.253+24756A>G		intron	N/A	ENSP00000465212.1
	ENSG00000267437	ENST00000587645.1	TSL:3	n.166-2277A>G		intron	N/A
	ZNF585A	ENST00000587817.5	TSL:2	n.338-15944A>G		intron	N/A	ENSP00000466825.1

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71119 AN: 151508 Hom.: 17088 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.470 AC: 71216 AN: 151626 Hom.: 17116 Cov.: 31 AF XY: 0.466 AC XY: 34493 AN XY: 74042

African (AFR) AF: 0.482 AC: 19909 AN: 41332

American (AMR) AF: 0.459 AC: 6983 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1536 AN: 3456

East Asian (EAS) AF: 0.150 AC: 775 AN: 5154

South Asian (SAS) AF: 0.399 AC: 1904 AN: 4774

European-Finnish (FIN) AF: 0.475 AC: 4983 AN: 10500

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.496 AC: 33687 AN: 67880

Other (OTH) AF: 0.496 AC: 1045 AN: 2106

Alfa AF: 0.476 Hom.: 5884

Bravo AF: 0.469

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.1
DANN	Benign	0.79
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs4805201; hg19: chr19-37622011;