chr20-37931757-C-A

Variant names:

• chr20-37931757-C-A
• rs199564199
• NM_080607.3:c.244C>A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_080607.3(VSTM2L):​c.244C>A​(p.Arg82Arg) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: VSTM2L NM_080607.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.33

Genes affected

VSTM2L (HGNC:16096): (V-set and transmembrane domain containing 2 like) Predicted to enable cell-cell adhesion mediator activity. Involved in negative regulation of neuron apoptotic process. Located in cytoplasm and extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VSTM2L	NM_080607.3	c.244C>A	p.Arg82Arg	synonymous_variant	Exon 2 of 4	ENST00000373461.9	NP_542174.1
VSTM2L	XM_011528530.2	c.244C>A	p.Arg82Arg	synonymous_variant	Exon 2 of 3		XP_011526832.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSTM2L	ENST00000373461.9	c.244C>A	p.Arg82Arg	synonymous_variant	Exon 2 of 4	1	NM_080607.3	ENSP00000362560.4
VSTM2L	ENST00000448944.1	c.244C>A	p.Arg82Arg	synonymous_variant	Exon 2 of 3	3		ENSP00000406537.1
VSTM2L	ENST00000373459.4	c.122-12224C>A		intron_variant	Intron 1 of 1	3		ENSP00000362558.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	11
DANN	Benign	0.66

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: rs199564199; hg19: chr20-36560159;