rs16946737

Variant names:

• chr16-77883969-T-C
• rs16946737
• NM_020927.3:c.883-639T>C

Variant summary

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

The NM_020927.3(VAT1L):​c.883-639T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,944 control chromosomes in the GnomAD database, including 28,654 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 0.60 (28654 hom., cov: 31)
• Consequence: VAT1L NM_020927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 4 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VAT1L	NM_020927.3	c.883-639T>C		intron_variant	Intron 6 of 8	ENST00000302536.3	NP_065978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VAT1L	ENST00000302536.3	c.883-639T>C		intron_variant	Intron 6 of 8	1	NM_020927.3	ENSP00000303129.2

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90816 AN: 151824 Hom.: 28650 Cov.: 31

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.598 AC: 90839 AN: 151944 Hom.: 28654 Cov.: 31 AF XY: 0.603 AC XY: 44788 AN XY: 74274

African (AFR) AF: 0.378 AC: 15657 AN: 41416

American (AMR) AF: 0.673 AC: 10283 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2557 AN: 3470

East Asian (EAS) AF: 0.662 AC: 3408 AN: 5150

South Asian (SAS) AF: 0.745 AC: 3583 AN: 4808

European-Finnish (FIN) AF: 0.696 AC: 7348 AN: 10550

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45852 AN: 67960

Other (OTH) AF: 0.607 AC: 1279 AN: 2108

Alfa AF: 0.626 Hom.: 11440

Bravo AF: 0.586

Asia WGS AF: 0.692 AC: 2405 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	1.7
DANN	Benign	0.30
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16946737; hg19: chr16-77917866;