rs1036229

Variant names:

• chr19-29489603-G-A
• rs1036229
• ENST00000804100.1:n.713C>T

Variant summary

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

The ENST00000804100.1(VSTM2B-DT):​n.713C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,974 control chromosomes in the GnomAD database, including 3,491 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 0.19 (3491 hom., cov: 32)
• Consequence: VSTM2B-DT ENST00000804100.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722
• Publications: 2 publications found

Genes affected

VSTM2B-DT (HGNC:27615): (VSTM2B divergent transcript)

LOC124904683 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804100.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSTM2B-DT	NR_040029.2		n.327+35821C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSTM2B-DT	ENST00000804100.1		n.713C>T		non_coding_transcript_exon	Exon 2 of 2
	VSTM2B-DT	ENST00000577849.3	TSL:3	n.435+35821C>T		intron	N/A
	VSTM2B-DT	ENST00000582581.5	TSL:2	n.329+35821C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29394 AN: 151856 Hom.: 3489 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.194 AC: 29431 AN: 151974 Hom.: 3491 Cov.: 32 AF XY: 0.197 AC XY: 14652 AN XY: 74294

African (AFR) AF: 0.294 AC: 12172 AN: 41408

American (AMR) AF: 0.190 AC: 2903 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 626 AN: 3462

East Asian (EAS) AF: 0.423 AC: 2174 AN: 5144

South Asian (SAS) AF: 0.253 AC: 1218 AN: 4808

European-Finnish (FIN) AF: 0.154 AC: 1626 AN: 10574

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8209 AN: 67972

Other (OTH) AF: 0.190 AC: 401 AN: 2112

Alfa AF: 0.138 Hom.: 2576

Bravo AF: 0.201

Asia WGS AF: 0.336 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.9
DANN	Benign	0.43
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs1036229; hg19: chr19-29980510;