16-77906637-A-G

Position:

• chr16-77906637-A-G

Variant summary

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

The NM_020927.3(VAT1L):​c.1077+21835A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,114 control chromosomes in the GnomAD database, including 3,729 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 0.22 (3729 hom., cov: 32)
• Consequence: VAT1L NM_020927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VAT1L	NM_020927.3	c.1077+21835A>G		intron_variant		ENST00000302536.3	NP_065978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VAT1L	ENST00000302536.3	c.1077+21835A>G		intron_variant		1	NM_020927.3	ENSP00000303129.2

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33199 AN: 151994 Hom.: 3727 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.218 AC: 33224 AN: 152114 Hom.: 3729 Cov.: 32 AF XY: 0.217 AC XY: 16169 AN XY: 74362

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.211

Alfa AF: 0.236 Hom.: 2055

Bravo AF: 0.206

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.74
DANN	Benign	0.35

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: rs10514431; hg19: chr16-77940534;