chr19-57825997-A-G

Variant names:

• chr19-57825997-A-G
• rs964795
• ENST00000593873.6:c.33+6052A>G

Variant summary

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

The ENST00000593873.6(ENSG00000268750):​c.33+6052A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,940 control chromosomes in the GnomAD database, including 24,807 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 0.57 (24807 hom., cov: 31)
• Consequence: ENSG00000268750 ENST00000593873.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 10 publications found

Genes affected

ENSG00000268750 (HGNC:):

ZNF587B (HGNC:37142): (zinc finger protein 587B) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

FKBP1AP1 (HGNC:3714): (FKBP prolyl isomerase 1A pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593873.6. 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
	FKBP1AP1	NR_024162.1		n.945T>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000268750	ENST00000593873.6	TSL:4	c.33+6052A>G		intron	N/A	ENSP00000469133.2	M0QXF5
	ZNF587B	ENST00000651253.2		c.33+6052A>G		intron	N/A	ENSP00000499083.2	A0A494C1I7
	ZNF587B	ENST00000594328.1	TSL:2	c.-115+5448A>G		intron	N/A	ENSP00000472004.1	M0R1N2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86057 AN: 151822 Hom.: 24770 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.567 AC: 86157 AN: 151940 Hom.: 24807 Cov.: 31 AF XY: 0.569 AC XY: 42248 AN XY: 74260

African (AFR) AF: 0.638 AC: 26445 AN: 41442

American (AMR) AF: 0.635 AC: 9688 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2010 AN: 3468

East Asian (EAS) AF: 0.643 AC: 3306 AN: 5144

South Asian (SAS) AF: 0.395 AC: 1903 AN: 4816

European-Finnish (FIN) AF: 0.574 AC: 6055 AN: 10556

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34908 AN: 67942

Other (OTH) AF: 0.577 AC: 1217 AN: 2110

Alfa AF: 0.527 Hom.: 14397

Bravo AF: 0.577

Asia WGS AF: 0.537 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.55
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

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

Other links and lift over

dbSNP: rs964795;

hg19: chr19-58337365;