rs10425935

Positions:

• chr19-29417200-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040029.2(VSTM2B-DT):​n.408-4234T>C variant causes a intron, non coding transcript 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 NR_040029.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

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=-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/exons	MANE	UniProt
VSTM2B-DT	NR_040029.2	n.408-4234T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VSTM2B-DT	ENST00000582581.5	n.410-4234T>C		intron_variant, non_coding_transcript_variant		2
VSTM2B-DT	ENST00000577849.2	n.408-4234T>C		intron_variant, non_coding_transcript_variant		3
VSTM2B-DT	ENST00000690107.1	n.401+11531T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0749

Gnomad4 NFE AF: 0.0934

Gnomad4 OTH AF: 0.174

Alfa AF: 0.117 Hom.: 2506

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10425935; hg19: chr19-29908107;