NM_003872.3:c.2045-17_2045-8delGGGTTTGTTT

Variant names:

• chr2-205763651-CTGTTTGGGTT-C
• rs2057860786
• NM_003872.3:c.2045-17_2045-8delGGGTTTGTTT

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP6

The NM_003872.3(NRP2):​c.2045-17_2045-8delGGGTTTGTTT variant causes a splice region, intron change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: NRP2 NM_003872.3 splice_region, intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 5.11
• Publications: 0 publications found

Genes affected

NRP2 (HGNC:8005): (neuropilin 2) This gene encodes a member of the neuropilin family of receptor proteins. The encoded transmembrane protein binds to SEMA3C protein {sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C} and SEMA3F protein {sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F}, and interacts with vascular endothelial growth factor (VEGF). This protein may play a role in cardiovascular development, axon guidance, and tumorigenesis. This protein has also been determined to act as a co-receptor for SARS-CoV-2 (which causes COVID-19) to infect host cells. [provided by RefSeq, Jul 2021]

NRP2-AS1 (HGNC:40415):

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 2-205763651-CTGTTTGGGTT-C is Benign according to our data. Variant chr2-205763651-CTGTTTGGGTT-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3353559.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003872.3. 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
	NRP2	NM_003872.3	MANE Select	c.2045-17_2045-8delGGGTTTGTTT		splice_region intron	N/A	NP_003863.2
	NRP2	NM_201266.2		c.2045-17_2045-8delGGGTTTGTTT		splice_region intron	N/A	NP_957718.1	O60462-1
	NRP2	NM_201279.2		c.2045-17_2045-8delGGGTTTGTTT		splice_region intron	N/A	NP_958436.1	O60462-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRP2	ENST00000357785.10	TSL:1 MANE Select	c.2045-22_2045-13delTGTTTGGGTT		intron	N/A	ENSP00000350432.5	O60462-3
	NRP2	ENST00000360409.7	TSL:1	c.2045-22_2045-13delTGTTTGGGTT		intron	N/A	ENSP00000353582.3	O60462-1
	NRP2	ENST00000412873.2	TSL:1	c.2045-22_2045-13delTGTTTGGGTT		intron	N/A	ENSP00000407626.2	O60462-2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	NRP2-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.1

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: rs2057860786; hg19: chr2-206628375;