NM_032414.3:c.199-189G>A

Variant names:

• chr1-110456043-G-A
• rs7513898
• NM_032414.3:c.199-189G>A

Variant summary

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

The NM_032414.3(PROK1):​c.199-189G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,058 control chromosomes in the GnomAD database, including 19,299 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 0.49 (19299 hom., cov: 32)
• Consequence: PROK1 NM_032414.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 4 publications found

Genes affected

PROK1 (HGNC:18454): (prokineticin 1) The protein encoded by this gene induces proliferation, migration, and fenestration (the formation of membrane discontinuities) in capillary endothelial cells derived from endocrine glands. It has little or no effect on a variety of other endothelial and non-endothelial cell types. Its expression is restricted to the steroidogenic glands (ovary, testis, adrenal, and placenta), is induced by hypoxia, and often complementary to the expression of vascular endothelial growth factor (VEGF), suggesting that these molecules function in a coordinated manner. [provided by RefSeq, Sep 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032414.3. 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
	PROK1	NM_032414.3	MANE Select	c.199-189G>A		intron	N/A	NP_115790.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PROK1	ENST00000271331.4	TSL:1 MANE Select	c.199-189G>A		intron	N/A	ENSP00000271331.3

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74986 AN: 151940 Hom.: 19280 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.494 AC: 75065 AN: 152058 Hom.: 19299 Cov.: 32 AF XY: 0.493 AC XY: 36625 AN XY: 74304

African (AFR) AF: 0.641 AC: 26577 AN: 41472

American (AMR) AF: 0.535 AC: 8185 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1522 AN: 3472

East Asian (EAS) AF: 0.558 AC: 2885 AN: 5172

South Asian (SAS) AF: 0.394 AC: 1898 AN: 4822

European-Finnish (FIN) AF: 0.391 AC: 4124 AN: 10556

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28218 AN: 67964

Other (OTH) AF: 0.479 AC: 1009 AN: 2106

Alfa AF: 0.457 Hom.: 2218

Bravo AF: 0.515

Asia WGS AF: 0.464 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.59
PhyloP100		-0.52
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

Other links and lift over

dbSNP: rs7513898; hg19: chr1-110998665;