NM_080607.3:c.121+5573A>G

Variant names:

• chr20-37909044-A-G
• rs6096822
• NM_080607.3:c.121+5573A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000305049 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080607.3. 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
	VSTM2L	NM_080607.3	MANE Select	c.121+5573A>G		intron	N/A	NP_542174.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSTM2L	ENST00000373461.9	TSL:1 MANE Select	c.121+5573A>G		intron	N/A	ENSP00000362560.4
	VSTM2L	ENST00000448944.1	TSL:3	c.121+5573A>G		intron	N/A	ENSP00000406537.1
	VSTM2L	ENST00000373459.4	TSL:3	c.121+5573A>G		intron	N/A	ENSP00000362558.4

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

African (AFR) AF: 0.312 AC: 12911 AN: 41428

American (AMR) AF: 0.0736 AC: 1125 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3470

East Asian (EAS) AF: 0.108 AC: 560 AN: 5170

South Asian (SAS) AF: 0.145 AC: 698 AN: 4818

European-Finnish (FIN) AF: 0.0859 AC: 911 AN: 10606

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0706 AC: 4802 AN: 68004

Other (OTH) AF: 0.116 AC: 245 AN: 2116

Alfa AF: 0.0926 Hom.: 1669

Bravo AF: 0.149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.76
PhyloP100		-0.11
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: rs6096822; hg19: chr20-36537446;