19-29401390-C-T

Variant names:

• chr19-29401390-C-T
• rs11669309
• ENST00000582581.5:n.602-2676G>A

Variant summary

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

The ENST00000582581.5(VSTM2B-DT):​n.602-2676G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,176 control chromosomes in the GnomAD database, including 2,751 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 0.17 (2751 hom., cov: 32)
• Consequence: VSTM2B-DT ENST00000582581.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.296 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSTM2B-DT	NR_040029.2		n.600-2676G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSTM2B-DT	ENST00000582581.5	TSL:2	n.602-2676G>A		intron	N/A
	VSTM2B-DT	ENST00000690107.2		n.402-8315G>A		intron	N/A
	VSTM2B-DT	ENST00000716172.1		n.449-9782G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26524 AN: 152058 Hom.: 2751 Cov.: 32

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.174 AC: 26541 AN: 152176 Hom.: 2751 Cov.: 32 AF XY: 0.179 AC XY: 13344 AN XY: 74384

African (AFR) AF: 0.0798 AC: 3313 AN: 41530

American (AMR) AF: 0.243 AC: 3713 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3470

East Asian (EAS) AF: 0.151 AC: 779 AN: 5162

South Asian (SAS) AF: 0.309 AC: 1487 AN: 4816

European-Finnish (FIN) AF: 0.248 AC: 2626 AN: 10606

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13372 AN: 67984

Other (OTH) AF: 0.162 AC: 342 AN: 2108

Alfa AF: 0.188 Hom.: 10875

Bravo AF: 0.166

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.87
DANN	Benign	0.35
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs11669309; hg19: chr19-29892297;