rs964795

chr19-57825997-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024162.1(FKBP1AP1):n.945T>C variant causes a non coding transcript exon 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: FKBP1AP1 NR_024162.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

Genes affected

FKBP1AP1 (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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FKBP1AP1	NR_024162.1	n.945T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF587B	ENST00000594328.1	c.-115+5448A>G		intron_variant		2
ZNF587B	ENST00000651253.2	c.33+6052A>G		intron_variant				A2

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

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.577

Alfa AF: 0.519 Hom.: 9476

Bravo AF: 0.577

Asia WGS AF: 0.537 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.5
Dann	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs964795; hg19: chr19-58337365;