rs6724852

Variant names:

• chr2-214561103-A-G
• rs6724852
• NM_001080500.4:c.521-14569A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-214561103-A-G
• chr2-214561103-A-T

Variant summary

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

The NM_001080500.4(VWC2L):​c.521-14569A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,132 control chromosomes in the GnomAD database, including 41,376 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 0.73 (41376 hom., cov: 32)
• Consequence: VWC2L NM_001080500.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 3 publications found

Genes affected

VWC2L (HGNC:37203): (von Willebrand factor C domain containing 2 like) Predicted to be involved in negative regulation of BMP signaling pathway. Predicted to act upstream of or within positive regulation of neuron differentiation. Predicted to be located in extracellular region and synapse. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000197585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VWC2L	NM_001080500.4	c.521-14569A>G		intron_variant	Intron 3 of 3	ENST00000312504.10	NP_001073969.1
VWC2L	NM_001345929.2	c.391-14569A>G		intron_variant	Intron 2 of 2		NP_001332858.1
VWC2L	NR_159945.1	n.1484-14569A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VWC2L	ENST00000312504.10	c.521-14569A>G		intron_variant	Intron 3 of 3	1	NM_001080500.4	ENSP00000308976.5
VWC2L	ENST00000427124.1	c.391-14569A>G		intron_variant	Intron 2 of 2	1		ENSP00000403779.1
ENSG00000197585	ENST00000412896.5	n.177+121979T>C		intron_variant	Intron 2 of 3	4
ENSG00000197585	ENST00000437883.1	n.133-87334T>C		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111373 AN: 152014 Hom.: 41346 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.733 AC: 111457 AN: 152132 Hom.: 41376 Cov.: 32 AF XY: 0.738 AC XY: 54865 AN XY: 74366

African (AFR) AF: 0.601 AC: 24916 AN: 41486

American (AMR) AF: 0.813 AC: 12430 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 2575 AN: 3470

East Asian (EAS) AF: 0.831 AC: 4304 AN: 5180

South Asian (SAS) AF: 0.805 AC: 3883 AN: 4826

European-Finnish (FIN) AF: 0.795 AC: 8403 AN: 10572

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52587 AN: 67994

Other (OTH) AF: 0.736 AC: 1555 AN: 2112

Alfa AF: 0.764 Hom.: 24478

Bravo AF: 0.727

Asia WGS AF: 0.814 AC: 2830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.013
DANN	Benign	0.68
PhyloP100		-2.1
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: rs6724852; hg19: chr2-215425827;