NM_020927.3:c.1077+21835A>G

Variant names:

• chr16-77906637-A-G
• rs10514431
• NM_020927.3:c.1077+21835A>G

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.247 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VAT1L	NM_020927.3	MANE Select	c.1077+21835A>G		intron	N/A	NP_065978.1	Q9HCJ6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VAT1L	ENST00000302536.3	TSL:1 MANE Select	c.1077+21835A>G		intron	N/A	ENSP00000303129.2	Q9HCJ6

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

African (AFR) AF: 0.204 AC: 8471 AN: 41496

American (AMR) AF: 0.153 AC: 2340 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 840 AN: 3466

East Asian (EAS) AF: 0.149 AC: 772 AN: 5180

South Asian (SAS) AF: 0.259 AC: 1247 AN: 4820

European-Finnish (FIN) AF: 0.239 AC: 2525 AN: 10568

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16364 AN: 67984

Other (OTH) AF: 0.211 AC: 445 AN: 2112

Alfa AF: 0.235 Hom.: 2262

Bravo AF: 0.206

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.74
DANN	Benign	0.35
PhyloP100		-0.72
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: rs10514431; hg19: chr16-77940534;