19-29412770-G-A

Variant names:

• chr19-29412770-G-A
• rs12986207
• ENST00000577849.3:n.712C>T

Variant summary

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

The ENST00000577849.3(VSTM2B-DT):​n.712C>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 0.146 in 152,358 control chromosomes in the GnomAD database, including 1,991 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 0.15 (1988 hom., cov: 33)
  • Exomes 𝑓: 0.15 (3 hom.)
• Consequence: VSTM2B-DT ENST00000577849.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 6 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577849.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSTM2B-DT	NR_040029.2		n.599+5C>T		splice_region intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSTM2B-DT	ENST00000577849.3	TSL:3	n.712C>T		non_coding_transcript_exon	Exon 3 of 3
	VSTM2B-DT	ENST00000804093.1		n.687C>T		non_coding_transcript_exon	Exon 3 of 3
	VSTM2B-DT	ENST00000804094.1		n.660C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22186 AN: 152110 Hom.: 1990 Cov.: 33

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.154 AC: 20 AN: 130 Hom.: 3 Cov.: 0 AF XY: 0.170 AC XY: 16 AN XY: 94

African (AFR) AF: 0.250 AC: 2 AN: 8

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.143 AC: 14 AN: 98

Other (OTH) AF: 0.167 AC: 2 AN: 12

GnomAD4 genome AF: 0.146 AC: 22180 AN: 152228 Hom.: 1988 Cov.: 33 AF XY: 0.145 AC XY: 10759 AN XY: 74428

African (AFR) AF: 0.0549 AC: 2280 AN: 41554

American (AMR) AF: 0.183 AC: 2798 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1056 AN: 5158

South Asian (SAS) AF: 0.160 AC: 770 AN: 4818

European-Finnish (FIN) AF: 0.104 AC: 1105 AN: 10600

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12563 AN: 68004

Other (OTH) AF: 0.192 AC: 407 AN: 2116

Alfa AF: 0.145 Hom.: 1190

Bravo AF: 0.150

Asia WGS AF: 0.167 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.43
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12986207; hg19: chr19-29903677;