chr16-77882294-T-A

Variant names:

• chr16-77882294-T-A
• rs435746
• NM_020927.3:c.883-2314T>A

Variant summary

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

The NM_020927.3(VAT1L):​c.883-2314T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,246 control chromosomes in the GnomAD database, including 5,632 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 0.26 (5632 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: VAT1L NM_020927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 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.883-2314T>A		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.883-2314T>A		intron	N/A	ENSP00000303129.2
	VAT1L	ENST00000563850.1	TSL:5	n.501T>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39753 AN: 152128 Hom.: 5618 Cov.: 34

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.241

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.262 AC: 39815 AN: 152246 Hom.: 5632 Cov.: 34 AF XY: 0.259 AC XY: 19297 AN XY: 74434

African (AFR) AF: 0.370 AC: 15369 AN: 41512

American (AMR) AF: 0.238 AC: 3636 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1808 AN: 5176

South Asian (SAS) AF: 0.141 AC: 683 AN: 4830

European-Finnish (FIN) AF: 0.227 AC: 2406 AN: 10596

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14616 AN: 68032

Other (OTH) AF: 0.249 AC: 526 AN: 2116

Alfa AF: 0.224 Hom.: 2282

Bravo AF: 0.269

Asia WGS AF: 0.241 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.28
DANN	Benign	0.59
PhyloP100		-0.71
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: rs435746; hg19: chr16-77916191;