19-29401390-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VSTM2B-DT	NR_040029.2	n.600-2676G>A		intron_variant	Intron 3 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSTM2B-DT	ENST00000582581.5	n.602-2676G>A		intron_variant	Intron 3 of 9	2
VSTM2B-DT	ENST00000690107.1	n.402-8315G>A		intron_variant	Intron 2 of 4

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

Gnomad4 AFR AF: 0.0798

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.162

Alfa AF: 0.190 Hom.: 5510

Bravo AF: 0.166

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11669309; hg19: chr19-29892297;