16-77934107-T-C

Variant names:

• chr16-77934107-T-C
• rs387138
• NM_020927.3:c.1078-37743T>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.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
• Publications: 7 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]

LOC105371351 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VAT1L	NM_020927.3	c.1078-37743T>C		intron_variant	Intron 7 of 8	ENST00000302536.3	NP_065978.1
LOC105371351	XR_007065123.1	n.1637A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VAT1L	ENST00000302536.3	c.1078-37743T>C		intron_variant	Intron 7 of 8	1	NM_020927.3	ENSP00000303129.2
ENSG00000294326	ENST00000722770.1	n.282+1848A>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.454 AC: 18808 AN: 41426

American (AMR) AF: 0.653 AC: 9976 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1893 AN: 3472

East Asian (EAS) AF: 0.664 AC: 3426 AN: 5162

South Asian (SAS) AF: 0.481 AC: 2314 AN: 4810

European-Finnish (FIN) AF: 0.546 AC: 5762 AN: 10550

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39288 AN: 67958

Other (OTH) AF: 0.577 AC: 1218 AN: 2112

Alfa AF: 0.572 Hom.: 46044

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
PhyloP100		-0.59
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: rs387138; hg19: chr16-77968004;