19-29376976-C-T

Variant names:

• chr19-29376976-C-T
• rs17624933
• ENST00000582581.5:n.2030+14445G>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.2030+14445G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,996 control chromosomes in the GnomAD database, including 9,859 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 0.35 (9859 hom., cov: 32)
• Consequence: VSTM2B-DT ENST00000582581.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VSTM2B-DT	NR_040029.2	n.2028+14445G>A		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSTM2B-DT	ENST00000582581.5	n.2030+14445G>A		intron_variant	Intron 9 of 9	2
VSTM2B-DT	ENST00000660387.1	n.1571+14445G>A		intron_variant	Intron 6 of 6
VSTM2B-DT	ENST00000690107.2	n.783+14445G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53302 AN: 151878 Hom.: 9850 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.351 AC: 53331 AN: 151996 Hom.: 9859 Cov.: 32 AF XY: 0.349 AC XY: 25918 AN XY: 74262

African (AFR) AF: 0.272 AC: 11291 AN: 41460

American (AMR) AF: 0.286 AC: 4367 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1071 AN: 3472

East Asian (EAS) AF: 0.409 AC: 2104 AN: 5142

South Asian (SAS) AF: 0.298 AC: 1437 AN: 4816

European-Finnish (FIN) AF: 0.389 AC: 4101 AN: 10548

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27639 AN: 67964

Other (OTH) AF: 0.345 AC: 729 AN: 2114

Alfa AF: 0.354 Hom.: 1735

Bravo AF: 0.345

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.45
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs17624933; hg19: chr19-29867883;