rs6096822

chr20-37909044-A-G

Variant summary

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

The NM_080607.3(VSTM2L):c.121+5573A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,106 control chromosomes in the GnomAD database, including 2,471 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 0.14 (2471 hom., cov: 32)
• Consequence: VSTM2L NM_080607.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

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]

LOC124904896 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VSTM2L	NM_080607.3	c.121+5573A>G		intron_variant		ENST00000373461.9
LOC124904896	XR_007067576.1	n.3371-2185T>C		intron_variant, non_coding_transcript_variant
VSTM2L	XM_011528530.2	c.121+5573A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VSTM2L	ENST00000373461.9	c.121+5573A>G		intron_variant		1	NM_080607.3	P1
VSTM2L	ENST00000373459.4	c.121+5573A>G		intron_variant		3
VSTM2L	ENST00000448944.1	c.121+5573A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21762 AN: 151986 Hom.: 2462 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0737

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.143 AC: 21799 AN: 152106 Hom.: 2471 Cov.: 32 AF XY: 0.142 AC XY: 10558 AN XY: 74376

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.0736

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.0706

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0854 Hom.: 1033

Bravo AF: 0.149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.0
Dann	Benign	0.76

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: rs6096822; hg19: chr20-36537446;