rs254770

Variant names:

• chr16-77843674-A-T
• rs254770
• NM_020927.3:c.579+18213A>T

Variant summary

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

The NM_020927.3(VAT1L):​c.579+18213A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,150 control chromosomes in the GnomAD database, including 5,658 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 0.27 (5658 hom., cov: 32)
• Consequence: VAT1L NM_020927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020927.3. 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
	VAT1L	NM_020927.3	MANE Select	c.579+18213A>T		intron	N/A	NP_065978.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VAT1L	ENST00000302536.3	TSL:1 MANE Select	c.579+18213A>T		intron	N/A	ENSP00000303129.2

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40670 AN: 152032 Hom.: 5654 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0788

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.267 AC: 40697 AN: 152150 Hom.: 5658 Cov.: 32 AF XY: 0.267 AC XY: 19835 AN XY: 74380

African (AFR) AF: 0.227 AC: 9409 AN: 41520

American (AMR) AF: 0.247 AC: 3774 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3470

East Asian (EAS) AF: 0.0786 AC: 407 AN: 5178

South Asian (SAS) AF: 0.189 AC: 913 AN: 4826

European-Finnish (FIN) AF: 0.370 AC: 3909 AN: 10576

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20192 AN: 67980

Other (OTH) AF: 0.268 AC: 564 AN: 2106

Alfa AF: 0.280 Hom.: 753

Bravo AF: 0.258

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.50
PhyloP100		-2.3
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: rs254770; hg19: chr16-77877571;