rs7256832

Positions:

• chr19-29403898-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.600-5184T>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 0.313 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 NR_040029.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VSTM2B-DT	NR_040029.2	n.600-5184T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSTM2B-DT	ENST00000582581.5	n.602-5184T>C		intron_variant, non_coding_transcript_variant		2
VSTM2B-DT	ENST00000690107.1	n.402-10823T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.308

Alfa AF: 0.274 Hom.: 3183

Bravo AF: 0.322

Asia WGS AF: 0.352 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7256832; hg19: chr19-29894805;