rs892073

Variant names:

• chr19-29421387-G-T
• rs892073
• ENST00000577849.3:n.515+7344C>A

Variant summary

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

The ENST00000577849.3(VSTM2B-DT):​n.515+7344C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0845 in 152,164 control chromosomes in the GnomAD database, including 611 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 0.085 (611 hom., cov: 33)
• Consequence: VSTM2B-DT ENST00000577849.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838
• Publications: 10 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VSTM2B-DT	NR_040029.2	n.407+7344C>A		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSTM2B-DT	ENST00000577849.3	n.515+7344C>A		intron_variant	Intron 2 of 2	3
VSTM2B-DT	ENST00000582581.5	n.409+7344C>A		intron_variant	Intron 2 of 9	2
VSTM2B-DT	ENST00000690107.2	n.401+7344C>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12861 AN: 152046 Hom.: 613 Cov.: 33

Gnomad AFR AF: 0.0843

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.0762

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

GnomAD4 genome AF: 0.0845 AC: 12860 AN: 152164 Hom.: 611 Cov.: 33 AF XY: 0.0851 AC XY: 6328 AN XY: 74402

African (AFR) AF: 0.0842 AC: 3493 AN: 41508

American (AMR) AF: 0.0545 AC: 834 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0433 AC: 150 AN: 3468

East Asian (EAS) AF: 0.201 AC: 1036 AN: 5166

South Asian (SAS) AF: 0.121 AC: 583 AN: 4820

European-Finnish (FIN) AF: 0.0629 AC: 666 AN: 10594

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0870 AC: 5915 AN: 68000

Other (OTH) AF: 0.0759 AC: 160 AN: 2108

Alfa AF: 0.0827 Hom.: 924

Bravo AF: 0.0805

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.74
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs892073; hg19: chr19-29912294;