16-77797979-G-T

Variant names:

• chr16-77797979-G-T
• rs2914451
• NM_020927.3:c.233+9064G>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.233+9064G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,004 control chromosomes in the GnomAD database, including 30,201 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 0.61 (30201 hom., cov: 32)
• Consequence: VAT1L NM_020927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 8 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]

LOC107984878 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VAT1L	NM_020927.3	c.233+9064G>T		intron_variant	Intron 1 of 8	ENST00000302536.3	NP_065978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VAT1L	ENST00000302536.3	c.233+9064G>T		intron_variant	Intron 1 of 8	1	NM_020927.3	ENSP00000303129.2

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92904 AN: 151886 Hom.: 30207 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.611 AC: 92917 AN: 152004 Hom.: 30201 Cov.: 32 AF XY: 0.613 AC XY: 45550 AN XY: 74282

African (AFR) AF: 0.367 AC: 15213 AN: 41430

American (AMR) AF: 0.644 AC: 9851 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2309 AN: 3472

East Asian (EAS) AF: 0.750 AC: 3854 AN: 5142

South Asian (SAS) AF: 0.652 AC: 3141 AN: 4814

European-Finnish (FIN) AF: 0.742 AC: 7840 AN: 10572

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48444 AN: 67970

Other (OTH) AF: 0.648 AC: 1366 AN: 2108

Alfa AF: 0.684 Hom.: 153207

Bravo AF: 0.597

Asia WGS AF: 0.683 AC: 2375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.65
PhyloP100		0.29
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: rs2914451; hg19: chr16-77831876;