16-77934107-T-C

Position:

• chr16-77934107-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020927.3(VAT1L):​c.1078-37743T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,970 control chromosomes in the GnomAD database, including 23,444 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 0.55 (23444 hom., cov: 32)
• Consequence: VAT1L NM_020927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594

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]

LOC105371351 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VAT1L	NM_020927.3	c.1078-37743T>C		intron_variant		ENST00000302536.3
LOC105371351	XR_007065123.1	n.1637A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VAT1L	ENST00000302536.3	c.1078-37743T>C		intron_variant		1	NM_020927.3	P1

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83438 AN: 151850 Hom.: 23431 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.549 AC: 83487 AN: 151970 Hom.: 23444 Cov.: 32 AF XY: 0.548 AC XY: 40715 AN XY: 74284

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.577

Alfa AF: 0.571 Hom.: 32993

Bravo AF: 0.560

Asia WGS AF: 0.548 AC: 1907 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	0.34
DANN	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs387138; hg19: chr16-77968004;