19-50655132-C-G

Variant names:

• chr19-50655132-C-G
• rs889132
• NM_001195076.2:c.68-918C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001195076.2(C19orf81):​c.68-918C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,994 control chromosomes in the GnomAD database, including 29,778 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 0.61 (29778 hom., cov: 32)
• Consequence: C19orf81 NM_001195076.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 2 publications found

Genes affected

C19orf81 (HGNC:40041): (chromosome 19 open reading frame 81)

SYT3 (HGNC:11511): (synaptotagmin 3) Predicted to enable several functions, including phospholipid binding activity; protein dimerization activity; and syntaxin binding activity. Involved in positive regulation of dendrite extension. Located in endosome. [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 (NFE) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195076.2. 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
	C19orf81	NM_001195076.2	MANE Select	c.68-918C>G		intron	N/A	NP_001182005.1	C9J6K1
	SYT3	NM_001424346.1		c.-154+2878G>C		intron	N/A	NP_001411275.1	Q9BQG1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf81	ENST00000425202.6	TSL:5 MANE Select	c.68-918C>G		intron	N/A	ENSP00000417035.1	C9J6K1
	C19orf81	ENST00000850965.1		c.476-918C>G		intron	N/A	ENSP00000521049.1
	C19orf81	ENST00000850964.1		c.68-918C>G		intron	N/A	ENSP00000521048.1

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92974 AN: 151876 Hom.: 29771 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.612 AC: 93007 AN: 151994 Hom.: 29778 Cov.: 32 AF XY: 0.615 AC XY: 45671 AN XY: 74266

African (AFR) AF: 0.407 AC: 16863 AN: 41438

American (AMR) AF: 0.695 AC: 10633 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2073 AN: 3466

East Asian (EAS) AF: 0.598 AC: 3086 AN: 5158

South Asian (SAS) AF: 0.679 AC: 3268 AN: 4816

European-Finnish (FIN) AF: 0.715 AC: 7538 AN: 10540

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47328 AN: 67970

Other (OTH) AF: 0.619 AC: 1306 AN: 2110

Alfa AF: 0.643 Hom.: 4036

Bravo AF: 0.602

Asia WGS AF: 0.622 AC: 2166 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	8.2
DANN	Benign	0.54
PhyloP100		0.16
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: rs889132; hg19: chr19-51158389;