19-29403898-A-G

Variant names:

• chr19-29403898-A-G
• rs7256832
• ENST00000582581.5:n.602-5184T>C

Variant summary

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

The ENST00000582581.5(VSTM2B-DT):​n.602-5184T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,144 control chromosomes in the GnomAD database, including 7,921 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 0.31 (7921 hom., cov: 33)
• Consequence: VSTM2B-DT ENST00000582581.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 7 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.414 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.600-5184T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSTM2B-DT	ENST00000582581.5	TSL:2	n.602-5184T>C		intron	N/A
	VSTM2B-DT	ENST00000690107.2		n.402-10823T>C		intron	N/A
	VSTM2B-DT	ENST00000716172.1		n.448+8877T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47555 AN: 152026 Hom.: 7909 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.313 AC: 47612 AN: 152144 Hom.: 7921 Cov.: 33 AF XY: 0.317 AC XY: 23615 AN XY: 74396

African (AFR) AF: 0.371 AC: 15388 AN: 41504

American (AMR) AF: 0.423 AC: 6464 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1507 AN: 5160

South Asian (SAS) AF: 0.374 AC: 1803 AN: 4820

European-Finnish (FIN) AF: 0.321 AC: 3401 AN: 10602

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17085 AN: 67978

Other (OTH) AF: 0.308 AC: 652 AN: 2116

Alfa AF: 0.275 Hom.: 4271

Bravo AF: 0.322

Asia WGS AF: 0.352 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.36
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs7256832; hg19: chr19-29894805;