19-29421387-G-T

Position:

• chr19-29421387-G-T

Variant summary

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

The NR_040029.2(VSTM2B-DT):​n.407+7344C>A 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 0.0845 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 NR_040029.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838

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=-0.82).
• 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/exons	MANE	Protein	UniProt
VSTM2B-DT	NR_040029.2	n.407+7344C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSTM2B-DT	ENST00000582581.5	n.409+7344C>A		intron_variant, non_coding_transcript_variant		2
VSTM2B-DT	ENST00000577849.2	n.407+7344C>A		intron_variant, non_coding_transcript_variant		3
VSTM2B-DT	ENST00000690107.1	n.401+7344C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0842

Gnomad4 AMR AF: 0.0545

Gnomad4 ASJ AF: 0.0433

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0629

Gnomad4 NFE AF: 0.0870

Gnomad4 OTH AF: 0.0759

Alfa AF: 0.0820 Hom.: 522

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs892073; hg19: chr19-29912294;