rs10425935

Variant names:

• chr19-29417200-A-G
• rs10425935
• ENST00000577849.3:n.516-4234T>C

Variant summary

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

The ENST00000577849.3(VSTM2B-DT):​n.516-4234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,030 control chromosomes in the GnomAD database, including 5,242 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 0.20 (5242 hom., cov: 32)
• Consequence: VSTM2B-DT ENST00000577849.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VSTM2B-DT	NR_040029.2	n.408-4234T>C		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSTM2B-DT	ENST00000577849.3	n.516-4234T>C		intron_variant	Intron 2 of 2	3
VSTM2B-DT	ENST00000582581.5	n.410-4234T>C		intron_variant	Intron 2 of 9	2
VSTM2B-DT	ENST00000690107.2	n.401+11531T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31103 AN: 151912 Hom.: 5226 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0749

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0934

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.205 AC: 31166 AN: 152030 Hom.: 5242 Cov.: 32 AF XY: 0.200 AC XY: 14896 AN XY: 74344

African (AFR) AF: 0.468 AC: 19394 AN: 41456

American (AMR) AF: 0.120 AC: 1831 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3472

East Asian (EAS) AF: 0.184 AC: 948 AN: 5156

South Asian (SAS) AF: 0.154 AC: 739 AN: 4794

European-Finnish (FIN) AF: 0.0749 AC: 793 AN: 10592

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0934 AC: 6347 AN: 67960

Other (OTH) AF: 0.174 AC: 368 AN: 2110

Alfa AF: 0.133 Hom.: 8764

Bravo AF: 0.219

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.37
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs10425935; hg19: chr19-29908107;