rs13330130

Positions:

• chr16-77796710-A-G

Variant summary

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

The NM_020927.3(VAT1L):​c.233+7795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,172 control chromosomes in the GnomAD database, including 4,449 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 0.22 (4449 hom., cov: 32)
• Consequence: VAT1L NM_020927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

VAT1L (HGNC:29315): (vesicle amine transport 1 like) Predicted to enable oxidoreductase activity and zinc ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

LOC107984878 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VAT1L	NM_020927.3	c.233+7795A>G		intron_variant		ENST00000302536.3
LOC107984878	XR_001752259.2	n.70-22689T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VAT1L	ENST00000302536.3	c.233+7795A>G		intron_variant		1	NM_020927.3	P1

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33411 AN: 152054 Hom.: 4431 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0830

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.220 AC: 33493 AN: 152172 Hom.: 4449 Cov.: 32 AF XY: 0.216 AC XY: 16107 AN XY: 74404

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0828

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.213

Alfa AF: 0.167 Hom.: 3135

Bravo AF: 0.234

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13330130; hg19: chr16-77830607;