19-29410843-T-C

Variant names:

• chr19-29410843-T-C
• rs8110188
• ENST00000582581.5:n.601+1932A>G

Variant summary

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

The ENST00000582581.5(VSTM2B-DT):​n.601+1932A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,054 control chromosomes in the GnomAD database, including 37,298 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 0.69 (37298 hom., cov: 32)
• Consequence: VSTM2B-DT ENST00000582581.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 1 publications found

Genes affected

VSTM2B-DT (HGNC:27615): (VSTM2B divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582581.5. 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
	VSTM2B-DT	NR_040029.2		n.599+1932A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSTM2B-DT	ENST00000582581.5	TSL:2	n.601+1932A>G		intron	N/A
	VSTM2B-DT	ENST00000690107.2		n.402-17768A>G		intron	N/A
	VSTM2B-DT	ENST00000716172.1		n.448+1932A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105181 AN: 151936 Hom.: 37248 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.692 AC: 105296 AN: 152054 Hom.: 37298 Cov.: 32 AF XY: 0.692 AC XY: 51468 AN XY: 74324

African (AFR) AF: 0.827 AC: 34293 AN: 41486

American (AMR) AF: 0.751 AC: 11482 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2510 AN: 3470

East Asian (EAS) AF: 0.570 AC: 2942 AN: 5164

South Asian (SAS) AF: 0.683 AC: 3277 AN: 4800

European-Finnish (FIN) AF: 0.661 AC: 6992 AN: 10578

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41527 AN: 67960

Other (OTH) AF: 0.697 AC: 1473 AN: 2112

Alfa AF: 0.640 Hom.: 55283

Bravo AF: 0.709

Asia WGS AF: 0.629 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.7
DANN	Benign	0.51
PhyloP100		0.0060

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs8110188; hg19: chr19-29901750;