chr16-77833311-T-C

Variant names:

• chr16-77833311-T-C
• rs10514430
• NM_020927.3:c.579+7850T>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.579+7850T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,184 control chromosomes in the GnomAD database, including 852 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 0.10 (852 hom., cov: 33)
• Consequence: VAT1L NM_020927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VAT1L	NM_020927.3	c.579+7850T>C		intron_variant	Intron 3 of 8	ENST00000302536.3	NP_065978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VAT1L	ENST00000302536.3	c.579+7850T>C		intron_variant	Intron 3 of 8	1	NM_020927.3	ENSP00000303129.2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15661 AN: 152066 Hom.: 850 Cov.: 33

Gnomad AFR AF: 0.0817

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0605

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.103 AC: 15668 AN: 152184 Hom.: 852 Cov.: 33 AF XY: 0.104 AC XY: 7721 AN XY: 74382

African (AFR) AF: 0.0818 AC: 3399 AN: 41534

American (AMR) AF: 0.0893 AC: 1366 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3472

East Asian (EAS) AF: 0.0601 AC: 311 AN: 5174

South Asian (SAS) AF: 0.103 AC: 495 AN: 4824

European-Finnish (FIN) AF: 0.162 AC: 1716 AN: 10582

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.113 AC: 7701 AN: 67988

Other (OTH) AF: 0.109 AC: 229 AN: 2110

Alfa AF: 0.0876 Hom.: 331

Bravo AF: 0.0983

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.43
PhyloP100		-0.45
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: rs10514430; hg19: chr16-77867208;